I dont know, how do you feel about this, but personally i always considered the available factions the single most important aspect of strategy games. I guess one may consider the scope of the game scale-wise and orientation toward either micro or macro to be even more important aspect, but nevertheless, the factions are very important, because psychologically they are all about identity.

Since the start of my gaming career i played quite a lot of strategy games, mostly RTSes, as they are my preference. It is for sure, that few of those games i liked, despite their factions felt sort of meh, cause i found them either not interesting enough, or not diverse/unique enough. But at the same time i think it its safe to say, my fav RTS games were the ones with factions, i considered exciting to just think about, not to mention play. Be it for their gameplay mechanics, which fit my playstyle, or rather what i basically see as cool, or for their cool and interesting units, sometimes purely from aesthetical POV ( i liked their looks LOL). Usually, it is/was the combination of these factors. Perhaps the most notable exception to this rule is Homeworld, which i liked mostly for its superb single-player campaign and overall artistic presentation.

Over the years i realized i usually tend to pick the alternative to the main faction of the game. If there are more than 2 factions (usually 3 or 4), i tend to go for the third or the last one. It largely depends on their characteristics, but these factions seem to be universally the ones, i find for some reason compelling - these factions tend to focus more on a finesse, high-tech or unique stuff, rather than brute-force or some standard generic units, and this i find appeasing. 

Lastly, obviously based on the previous paragraph, i believe there is a pattern in how factions in games are designed, clearly there are certain tropes (starcraft being the model one), which the game-designers usually follow, even though sometimes these are bit mixed to achieve at least some impression of variety and novelty. I guess i think this is an approach, which works quite nicely, even though sometimes bit more of an innovation would not hurt. Anyway, Sins itself is a good example of this approach, while its factions certainly differ enough from those in StarCraft or other similar games, there is a lot of stuff there you would expect to be exactly the way, it is. TEC for example, despite being somewhat modeled as the zerg-like faction with their cheap units and strong sway toward economy/production, are visually the quintessential Terran faction. Basically no surprises there.

One game i found a bit weird in this regard, was Universe at War. Ultimately it was not a bad game, and i liked its visual design, but the factions...were completely uninteresting to me. Only the mechs of Hierarchy were somewhat cool... but other than that? No proper aircraft, naval units or space-ships, just bunch of generic troops or drones/hovercraft. And then some weird fantasy-like faction with no visually appealing stuff? No, thank you.

The other games i´d like to mention:

Dune 2 - my first RTS games. The factions were not really diverse enough, so i did not have clear favourite. Probably Harkonnen cause of the Rise of the Harkonnen song, lol. And i like red color.

Warcraft 2 - detto. Was a great game and i loved its graphics, but the factions were not particularly unique.

Warcraft 3 - found myself playing for the Night Elves (3rd of 4 factions) for some reason. Humans and Orcs were meh, generic and boring, while Undead looked cool, but i dunno, did not fit me well. 

Age of Empires series - too many nations with not enough differences IMHO. Be it gameplay-wise or visually. Few specific units based on history were not enough. I missed the Age 3 datadisc though, which apparently added some cool and unique stuff/mechanics and improved the diversity a lot. Otherwise, safe to say, not a big fan of Age series.

Starcraft 1/2 - Protoss for their high tech stuff and orientation on air units. I was fond of Terrans as well, the only faction i was not really into, were Zerg. Organic bio-shit does not excite me one bit, i guess. Carriers or Battlecruisers are where its at. Ultimately not really a game for me though, as it caters to competitive players and their preference for 10 minute long matches, almost sports-like. I need immersion and epicness.

Command and Conquer - Never really liked GDI, nor NOD. Classic game with boring factions. Lack of air units, no navy. GDI the most generic modern-warfare faction ever, NOD weird, not terrorist-like at all, with weird, rather than cool units. Red Alert so much better.

CnC3 - Scrin, obviously, since never liked other 2 factions. And i actually liked looks of their stuff and they had lot of cool units, like Annihilator Tripods, those Airborne Carriers and Mothership! Hell yeah.

Red Alert - The first one was the best IMHO. I wonder which faction would you consider to be main of the 2? Allies clearly the western one, but the game was called Red Alert, so to me the Soviets were the default one. Pretty sure their brute force approach appeased to majority of players as well. Not me though, LOL. Cruisers, Spy Satellites, Gap generators, Chronospheres - that was my thing. I remained Allied player for the other 2 games as well, since they added some cool air units, like for example Century bomber or Vindicator. 

Generals/Zero Hour - i guess the US were the main faction,  and they were my fav, So to certain extent, this was different, meant as the main faction was a high-tech one here. Zero Hour was even better, I loved Air Force General the most. Death from Above ffs. But the other factions in these games were cool as well. Diversity at its finest.

Dawn of War series - I was never much into Warhammer, so i hesitated to give it a try at first. Eventually i found out its pretty good game and for some time, played it a lot with my buddy. But its true i did not really have fav faction, the game itself was great for its gameplay, but the factions, were meh. I played for Chaos at first, as they were opposite to the Space Marines and their Cultists were hilarious with all the "Chaos is strong" hehe. With Dark Crusade coming out i moved to Necrons and they were way more exciting, Tau were cool as well, with all their great machinery, gunships and shit, but my buddy already chose them, so i went with Crons. Not that i regret, their ressurectable units and the summonable C´Tan god were too cool. And the best of all - the Monolith! Best HQ building ever!

Supreme Commander - cool game, factions not unique enough for me to choose, despite all having exciting air and naval units. I guess in original game i prefered Aeon, since they seemed to be most navy-oriented, while in the SupCom 2 i played more for Cybrans, mostly for cosmetic reasons. I guess walking ships might have something to do with it, Not that i like them, conceptually, actually i thought walking ships are the worst idea ever. But they worked quite fine.

Conquest Frontier Wars - I played Celareons. Was bit unhappy with their lack of fighters/carriers, but i liked their shiny ice/water like ships, reminding me of Taelon stuff from the Earth-Final Conflict TV show. And they had great defenses, Proteus Missile Platform, Hydrofoil AA Defense, Starburst. And how about fleet of cloaked Auroras backdooring via Portal artificial wormhole into enemy home system, fuck yeah! Brilliant game this.

Earth 2160 - the Aliens over anyone else. Their unique cloning mechanic was fun to play. And their huge Postomor Battlecruisers ravaging enemy bases...yes please. 

Company of Heroes - good game, but prefered Dawn of War lot more. Neither Allies or ze Germans were really interesting, cause of the game focus on small infantry/tank skirmishes. Differences between factions IMHO too subtle. But i never played it enough to judge it deeper.

Sins/Rebellion - clearly Vasari fan here. From the first moment. Vasari Loyalists probably my most fav faction in any game i played, since the other factions dont really have anything, i would terribly miss playing for them. In Red Alert for example playing for Allies i wished i had Soviet Migs, no such situation occurs here. The only exception being perhaps VR jumping bases. Does not mean other races dont have some cool stuff themselves. But i am simply totally cool with how VL were designed. Not to mention i liked the looks of their units the most. Especially the quintet of Vorastra - Kortul - Vulkoras - Ruiner - Orkulus does it for me. Keep these in Sins II please! 

These are the most notable games i played and have opinion on them, What are yours? What do you like, prefer? Be it in these games i mentioned, or some others, you personally favour? Or generally speaking? I am eager to hear.