I have read through this, and i strongly disagree with some of your suggestions and in general I think this kind of thing needs some descriptive rationale rather than just suggestions.   Still, you obviously put some thought into this.  Anyways, here's my comments:

A number of the spells you listed I have no opinion on, because I have not used them enough.

I have never understood the confusion spell

I got the idea that shadow world would release a ravaging horde of monsters hostile to everyone, I am not sure where you got the idea that "destroying everything in its path" would not include you if you were in its path.

I think heal is strong enough already.  It's enough to turn a lost battle into a safe win, so making it stronger seems cheesy to me.

I was expecting the "annointed by ___" line of spells to have a sustained mana cost and be dispellable.  But since turning a character into an effective caster needs a lot of work (reducing mana costs, increasing spell mastery, and for real effectiveness: building up initiative) I am not too worried about this one.

I think blindess is fine right now, but I think there should be a remove blindness spell (which must overcome the resistance of the caster, if the caster is still alive).  Turning it into a spell that's only good for short battles seems like a bad move. If you can't end the battle quickly, yourself, you should expect to get owned by the magic users (assuming they have the power to keep casting).

I think destiny's gift is too cheap - I think it should have a higher cost than celerity, but your suggestions might also work.  It should also have a cooldown.  Without a cooldown you can hold off using it until a particular champion needs it for a particular battle - you can just spam it until you get the effects you need.  With a cooldown you have to plan ahead (or only use it on a single target) and with a higher mana cost you'll have to be giving up significant capability.  

I think burning hands is fine - I think it's mostly for use against inflammable creatures (like trolls) when flame dart is on cooldown and a few other narrow niches like that.

Pandemonium seems to be bugged, in that after a few casts it just gives a visual effect and does not do anything but gives you no messages about this issue.  I am not sure what its tactical value is supposed to be.

I disagree with time limits for any spell that can be cast on the strategic map (like cloak of thorns).

I think that nerfing cloud walk without also nerfing call of the titans is silly (call of the titans has a 10 turn cooldown but every champion can cast it without needing any spell casting ability, so if you have 10 champions you can cast it 10 times in one turn though, granted, you will need to wait 10 turns before you do that again). Anyways, if you want to nerf cloud walk I would just increase the mana cost.  But I would rather see it only work on the caster than any of your suggestions.

Since shadow bolt does about the same damage that a flame dart does when flame dart gets resisted, I think it's fine.

I think they intended sunder to work like it does - it's removing the connection that keeps the elementals anchored to this plane of existence, and that's all it does - it needs to be powerful since it is so specialized.  Have you played the scenario, there's some text in it that refers to sunder.

Spell Leech needs AI fixes -- the problem right now is that the monster keeps trying to cast, it should go off and do a real attack if you leech it.

I see nothing wrong with thunderstrike - it's a fun spell - why do you want to change it?

First, generally speaking, magic is extremely powerful, and it's not all about the tactical damage. I think that a general theme of your suggestions has been to try to balance spells for tactical damage, and I think you are missing out on how the spells are useful.  Water is about control spells and the tactical mana cost reduction from mantle of oceans is incredible - that alone is almost worth the entire spell tree.  Thinking about it, pandemonium is probably for meant for breaking up the coordination of massed armies.

Second, a part of the dodge stacking issues are that the AI is so stupid, and is not prepared to deal with a game that lasts that long.  This is a shame, but there's so many things going on there and "fixing it" would involve a massive set of changes to the game, including victory conditions fixes, and several iterations of AI rewrites and upgrades.  Still, if you really want to fix dodge stacking issues, I think I would place a limit on dodge stacking (perhaps based on the level of the unit in question).

Third, I think it's good that some spells are level based and others are shard based, since this opens up different styles of game play. And in particular, I am disappointed in the entire player base for not properly investigating oracle ceresa's spell to corrupt shards.  Seriously, that's an awesome ability which is ruined by a game breaking bug.

It's awesome not just for offensive reasons, but for defensive reasons, and it's one of the big counters for dodge stacked archers. Wither, and Blood Sigil *reduce the attack* of enemy units.  You know how awesome a +1 attack is, with stacking?  Well these spells reduce the attack of those units. With stacked death shards you can mostly ignore enemy soldiers.  But almost nobody has even tried.

The thing is, there's a game breaking bug in blood sigil, in 1.02.  When the battle starts, it wants you to target an enemy unit (which is bogus since it is supposed to hit all enemy units), furthermore, targeting an enemy unit does nothing (which makes sense, since it's not a targetable spell) and the only way out is autoplay.  But even with autoplay another problem occurs - after some amount of game play the wither effect just stops happening at all (for me this was about when I hit level 10).

So, anyways, since almost nobody has even tried stacked death shards, I think that it's silly to talk about balancing death magic. Balancing needs to be based on the voice of experience, and this bug tells me that our player base does not have that experience.

Anyways...

The top level spells are mostly strategic in character, and help the magic heavy player own the map.  The damage spells, in particular, are another alternative for dealing with dodge stacked units.

Burning hands is an offensive spell with a cooldown independent of flame dart. Yes, it's close range, but that's ok, because it's a lower level spell.  If you get some fire shards and stack some spell mastery it does plenty of damage.

And, yes, roads with stables and a mounted army can get you a an effective move of 32 tiles. If you add the +1 move boots and a single champion with tireless march, this becomes a move of 48.  Granted, this is sticking to the roads, but those roads lead to the places you want to defend.  So cloud walk seems balanced with that (especially since it's only on the unit which contains the caster).

See above for my discussion on death shards and level based spells.  When they fix the UI bug with blood sigil, you really ought to try it with stacked death shards... I am sure there will then be cries of "stacked death shards are overpowered", but really it's just another strategy.  "Overpowered" typically seems to mean "beats my boring strategy and beats the lame AI". I really want the AI to get some massive improvements before any changes to skills get implemented to compensate for its failings.

And for sunder, it changes the battle field, nerfing summoned elementals in opponent armies and making clearing some wildlands easier. But that by itslf is not justification for a nerf. Nerfs are supposed to make the game fun, not remove magic specialization as a viable strategy.  I could maybe see increasing its mana cost, but I see nothing thematically wrong with a high level mage being able to dispel the magical bosses and (if they can survive long enough) assassin demons - if this is a problem at all I think it's a problem because we need additional end game content.  Those magical bosses are designed to look impressive but be beatable, they do relatively low damage and have low initiative and so on.

First, in the tactical sense, wither has a counter, several actually.  It does nothing about damage mechanisms that are not based on attack (spells), and it's not much use against a single unit with a high attack.  You can also bring in summons after it takes effect (which can be important for city assault under blood sigil).  If you are desperate you might also be able to pull something off with high health and reflection.  But it's big weakness is its cooldown, if you have two armies in the field, only one of them can be withered, and three armies makes it even easier.  Blood Sigil is different but you can pull the army out into the field by taking down unprotected death shards, which also weakens the effect.

Chaos is useful when you are desperate and hoping to get lucky.  The dazed effect is great, and so are some of the other effects.  And I think the damage is not resistible (and the damage variant seems to become extra probable when you hit a severely damaged unit with it).  I am thinking Pandemonium is for when you are facing a large army and do not have any better options but if you have something that takes all your enemies down to low health and if pandemonium's odds are like those of chaos, it might be a great finisher also.  But the really powerful early water spells are slow and mantle of oceans.  Also, tidal wave can also be impressive in the right circumstances (you can hit enemy territory with it, if there's an ocean handy).  And blizzard is a nice late game combat, and Vetrar's Howl can be incredibly powerful if you choose the right moment to use it. Also ice elementals are nice crowd control when you are fighting magic immune monsters, since their freezing cold slow-on-hit effect still takes effect (assuming you can keep the elemental alive long enough to hit anything).  And, finally, stinking mud is amazing crowd control for a warlock/evoker type channeler.  And spell leech would be great fun if the AI was not so blindly persistent in retrying a failing approach.  And Gentle Rain can be incredible if you have cities with enough essences to support it (in my current game, the maximum I have seen is 1 essence in a tile that will support a city)

But also note that the game has different settings, and on the settings I play on the shard based spells can sometimes out-power the level based spells.

But I do not see the appeal of making spell rank a determining factor.  For that to be balanced, the spells would have to be almost useless without the last rank, and if you are going to do that, it seems like just making the spells only be available in the last rank would accomplish something similar.  

If the problem with sunder is the high exps you can get, I think the solution would be to nerf the exps, not the spell.

And for the speed issue, I think there you are describing a custom mod, but another way of achieving that end would be to play on something like the settings I am currently using:

Huge map, swamp, many wildlands, no champions, balanced quests, insane difficulty, dense monsters, epic pacing, moderate magic strength (I thought I had selected sparse, but when I went into a new game to see my settings I see that it's on moderate -- oh well...), sparse resources, more often random events, and four sovereigns (Emperor Karavox, Magnar, Oracle Ceresa, and Warlord Verga). I am playing Amarians with a tailored variant of Lady Procipinee. Victory conditions are military and diplomatic, not the other two.

I do not know if I will survive, but it's going to be fun finding out...

Anyways, if mana is hard to come by and opponents are many and powerful, sure you can cloud walk, but not often enough, and the mana costs are going to hurt if you are not exceptionally sparing with it.

Anyways, I also like epic scale games, and I have found that the game gets boring (too easy) after a while, so this is my way of addressing that issue.