I my opinion this kind of map balance issues like Darvin3 describes will be neutralized by the law of large numbers. sure in one game your opponent has the advantage but in the next it's probably on your side. and over thousands of games it will just be spread evenly.
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I'd have to disagree; having 300 games that favour you, 300 games that favour your opponent, and 400 even games is NOT good game balance. The games that favour you don't "neutralize" the games that favour your opponent, since both cases are unfun for both parties involved. It's no fun for me when my opponent is a disadvantaged punching bag or when I'm struggling just to survive.
Within a single match, large numbers also don't apply. The two big factors are neutrals and start locations. The planets immediately surrounding your start location have a massive influence on your early game potential, which in turn has a massive influence on your late game potential. The second issue, as I mentioned, are neutrals, which usually number no more than two gravity wells per player.
IC surely could try to make a perfectly balanced game, where all factions are equal and all maps are absolutely symmetric for all players. But that would lead to an extremely boring RTS where the fastest-clicking guy wins (like in most other RTS).
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You don't need "perfect" balance, what you need is approximate balance. The problem is, as I mentioned, it doesn't take a whole lot of extra militia or missing extractors to give one player a significant disadvantage. A good example is cynosian rift; right next to your start location is an asteroid, an ice world, and a single random world. If my opponent gets a terran with only 5 defenders and I get a desert with 15 or so, it's going to be nearly impossible for me to win, since he'll likely be colonizing it by the time I get a scout over there to know what's going on!
Secondly, the "fastest clicking guy" is largely a misconception. I taught most of my friends how to play RTS, and none of them had any problem with speed. In fact, for the most part they tried to click faster than me with disasterous results. My first piece of advice to new RTS players is to slow down: learn to do things right, and then speed it up to a level at which you're comfortable. Good technique will absolutely steamroll someone relying on sheer speed. The simple truth is that micromanagement is about executing tactics and strategy. Quick execution is, of course, an advantage but it won't help you if your opponent has a superior strategy or set of tactics.
As analogy: imagine a Texas Hold em Poker game where each player gets the same pocket cards!
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In poker you play multiple hands; in Sins you basically get one hand and that's it.