This is actually OT but I assure you I've won many a game of eclipse even before the expansion and even without plasma missiles, which are nice but far from game winning. Literally. I've rarely seen anyone that spent much in fleet upgrades actually winning a game! It's more a case of a perceived unbalance... But to explain why I 'd need to derail this convo even more.
But then again, balancing a single item is never a problem. We're talking about balancing all civs so they can compete against each other so that each choice is viable or any other empty modern buzzword.
OT for Eclipse: Board game balance in general can be hard to talk about because the way a game is played can be so thoroughly rooted in a game group. Board games are slaves to meta in a way that video games aren't. For example, some people in my group want to ban the Planta from Eclipse because they think they're way too powerful. Of course they aren't too powerful, but a lot of the people in my group aren't very aggressive and so are generally more likely to let a Planta player expand to ridiculous amounts before they do something about it. This leads to a situation where Planta are not overpowered except for in my circles where they are. That being said, I definitely agree about plasma missiles. They're incredibly powerful in combat, potentially, but the challenge is taking that incredible power and turning it into victory points - and more importantly, turning it into more victory points than what you could have gotten investing your resources elsewhere.
Also, quick digression about Eclipse. The game always impresses me with how easily people pick it up. People who find games like Puerto Rico or even Catan too complex will still have a blast with Eclipse, despite it being far more complex than those games. I've begun to realize that the way a game presents itself and is explained can have a much larger impact on how complex or simple it seems than the actual rules and mechanics. The Europa Universalis games come to mind as PC games that seem much more complex than they actually are due to presentation and interface. Not to mention the sheer overwhelming nature of having literally hundreds of countries to choose from. IMHO Dominions is a fair bit more complex than EU but seems simpler and easier to pick up at first, just because of the nature of the game.
In any case, I think the issue is that we've been talking past each other in terms of balance. For me, balance is essentially making sure that everything works the way it should and does what you'd think it'd accomplish. In AoW 3, Rogues kinda struggling against Necromancers and Theocrats getting a nice healthy buff against them is the fun sort of imbalance. It broadens the game and it makes things more interesting. Beyond that, it makes sense. It's logical that someone who relies on poison and pinpointing vital organs would have a harder time against poison-immune, vital-organ-free Undead, and that someone who conjures up holy energy to smite the unnatural would enjoy an edge against the Undead. And I get your point that in a truly competitive environment, those things would be issues, and I think that's true, and in that sense, I can see how competitive balance can weaken the game. On the other hand, things like Necromancers being able to take control of Undead units, or reanimate dead ones under their control. That's something that is a pretty cool concept and isn't necessarily a balance issue - until you combine it with the fact that there are tons of high-tier wandering Undead monsters in most RMG games. Then it becomes an issue, because it's trivial for a Necromancer to amass a huge army of T4 units long before other players are even looking at T3, and at that point you're pretty much screwed. To me, that's the sort of imbalance that isn't fun.
TWT is another good example. It wasn't a case of certain races being over or underpowered in certain scenarios or for certain matchups. It was a case of certain races just being crap all the time, and certain races being too good all the time, largely due to things not working the way they should. In theory, Goblins lent themselves to low-cost swarms of units, for example, but in practice, production speeds and the upkeep system prevented that from actually being a thing. This generally just meant the Goblins were boring to play. And sure, I guess you could still have fun with them if you were into cherry tapping, but that always felt a bit pointless to me.
Or take a look at MoO. The fact that racial combat boosts, for example, are so underwhelming makes the game more boring, IMHO. I guess it can make the discovery thing slightly more fun? But discovery is only fun the first time. After that, you're just left with options that you'll never pick unless you're deliberately gimping yourself - and like I said, cherry-tapping only gets you so far. Now, combat boosts being less efficient than UniTol isn't really a balance issue, IMHO. The issue is more that the boosts don't really do much at all, and players will take them with a certain idea or concept for a race in mind and then be disappointed because these bonuses don't work the way you'd expect. Not every strategy should be equally viable. Not every strategy should be viable at all. But most strategies should behave the way the game indicates they'd behave. Significantly amplifying the combat boosts you can get from racial picks probably still wouldn't make them top-tier choices by any means, but they would mean that designing a warlike faction could be a lot more fun.