There already is manufacturing and research overflow. Excess points are saved and spent on your next turn. Unfortunately, the game does not tell you how much you have saved up, but  I guess we can't have everything. If I have 20 manufacturing and I build 2 Research Laboratories, after I finish the first one, the 10 extra manufacturing is saved up and the 2nd one will finish in 1 turn, although it will tell you that it will take 2 turns.

if you have 200 manufacturing and you build 10 ships that cost 100, the next 10 ships can be built with your saved up overflow. 

If you hover over the blank space in your manufacturing queue it will display how many points are accured. I don't know if this information is availabel for the research screen.

1. No micro needed they over flow. Initially they didn't, then they changed to end of next production, now all points are kept but you are limited to one item per turn. 

3. There is a request constructors button that sends an idle constructor to the starbase and if it's not available queues up a constructor at the nearest starbase. 

Your points are well taken.  On this one though, I think the AI will get a lot better as time goes on.  I feel like with the Ideology system and more adjacency/building choices there are a lot of fairly fat-tail min-maxing strategies that a player can do which hasn't been built into the AI very well yet.

Compared with GC2 where the strategic landscape with a lot flatter with much more straightforward risk/reward and investment metrics, GC3 has a whole lot of snowballing features that are built in.  This is to say, GC3 is a lot more dynamic and will ultimately be a MUCH more engaging platform, but on the other hand there are a couple of issues inherent in this environment:

1. countering - both for the player and the AI, it's not nearly as straightfoward to counter a snowballing enemy when they've been continually doubling down on a strategy that you don't necessarily have a terrific answer to anyway.
2. Focus & difficulty.  - it inherently makes investment choices much more important (especially in the early/mid game) because that's where these choices will determine when you hit your power curve and how fast it takes off.   So for players it can make it seem confusing and be continually behind if the AI is good at doubling down and snowballing the shit out of players...  (sort of like when I started playing GC2 and couldn't figure out how the stupid Torian's always had so many planets filled with people (er... frogs))..

it will be interesting to see how this dynamic is addressed, snowballing is always a mainstay mechanic of 4x games, but there really are mechanics in GC3 that can make it pretty unreal.

One possible solution to this would be to make the universe less habitable.  This was the game design for 'Fallen Enchantress' - though I didn't play nearly as much FE as GC2, the 'game difficulty' setting for FE wasn't just how strong the MOBs were that were wandering around, but also how much they would gang up on any player who started getting ahead to keep the world balanced (it was a frustrating world to play in, btw).  In this vein I see a few possibilities:

1. Military empires - let military technology diffuse to the pirates in their sector (ie pirates blow up your ships or see your frigates and figure out how to build better weapons/armor).  Let minors do likewise - this would insert military threats into military empires and keep all races at a more or less equally frustrated by pirates/minors.
2. Trade empires - your routes become targets of pirates, the more trade routes you have the bigger target - also with more trade routes maybe other races, outlying planets, minors etc get jealous and demand a cut of the trade routes passing by their systems.
3. Research/Economy empires - become espionage targets (although espionage isn't in yet).  The more facilities you have the more difficult it is to safeguard all of them, and the more easily their complexity can be disrupted.
4. Morale/Influence empires - Maybe a higher likelihood that some of your people see that simpler is better and want to flip back to "simpler" empires -- such as America's infatuation with Tibet.
5. Fast Expansion - too many people and planets and the more diseases/pestilence you run into - I see that there is some sort of disease mechanic built into GC3, but I haven't had much interaction with it.

The point is, that there are ways to quash the snowball that don't involve counter-snowballing - I think that a lot of it is tweaking/balance though - a lot of them seem to be straightforward mechanics in and of themselves..

I've only played a couple of games too and have largely come to the same conclusions that you have come to, but also, the last time I fired it up was back in beta 2 or 3 I think and it's really come a long long way and a lot of it is just polish at this point..

cheers,