I tend to play Evil 70% of the time, Neutral 20%, Good 5%. Neutral definitely has its place on smaller maps. Good was starting to hold its own when DA had the defense bug (some experiments suggest DA still has it).
Actually, in a lot of my DA games, over half my game I'm not any alignment at all. I tend to postpone researching Xeno Ethics a lot, because once you research it you don't get the ethical events when colonizing new planets. That means you miss out on a lot of Evil bonuses. It can still be worth it if you still choose Neutral (where the bonuses are immediate), but with Evil, a good portion of the game where you really are Evil, the game's already more-or-less over.
In regards to Evil's free invasion tactics, that's only true on large maps. You have to build the No Mercy Invasion Center, which is very expensive (I think it's like 2500bc?) and it's at the end of the Evil tech tree. It takes like 4 Information Warfares to get any return on your investment, not to mention you're tying up a planet tile and that planet's production for ~14 turns. I usually play Medium maps and I never build it.
The other key bonus to Evil is building the Artificial Slave Center, which gives you a big military production bonus. It goes together with the Mind Control Center nicely. Also, Evil is better at spamming starbases, because they don't pay for upgrade costs (in addition to building constructors twice as fast as everybody else).
Good probably does better on fast techs (e.g. Battle of the gods, Accelerated start, fast tech research), because the defense bonus kicks in. By contract, Evil effectively doesn't have a weapons bonus when all the techs are researched.