As for the alignment changes, I'm not against Drath as Neutral. But somehow making the Terran Good just isn't right. I didn't get an answer when I asked about why we need to keep the alignment count balanced. Anyone tried it with an unbalanced count?
I think the overall intent is to equalize the distribution of misaligned faction when starting a game against random enemies. You see, the whole diplomatic system revolves around giving causes for conflict, too much stuff to go into detail now, but there's alot of things there. Otherwise it might get boring on some game if you consider how much freedom is granted for the setup. You may start an all-uncommon huge galaxy against 2 factions, and when they all share your alignment then Wars may never break out. But the function of the AI is also to kind of stress the player, otherwise it's not challenging anymore.
But it could be done easily, what matters is the overall balancing. On that note, if we include Minors, Neutral is already in favour because most Minors are neutral. You could go with only 3 evil races, perhaps Korx or Yor, but then, the remaining evil races should see some love to compensate their relative strength.
On the Super Ability, that lets me change to a different SA, which may be a better solution than nothing. I was hoping for a way to change the attributes of ab SA. I.e. make the speed limit of Isolationist greater than 3.
I'm afraid that's not possible. SA are hardcoded, although some can be worked on via secondairy means, ie. Drengin Dominator Corvettes can be changed, Korath Spore Module, Trade/Spy/X-Col Techs could be changed, but many other things which directly interact with game mechanics are untouchable.
I also think that Isolator is a rather weak one, personally I'd actually increase it to 2. Although it is fun to play with it esp. if you build additional MSB in order to slow down ships to 1 speed. I remember I had to do that on my first Suicidal warfighting game as it was the only way to survive.
You can actually circumvent it a bit by using Fleet War Bubbles.
One other bad tendency I noticed: many races build Research Coordinator as the only research improvement on a planet. (Yes, I realize that the Capitol produces a few RP.)
On this score, there is one aspect of Tolmekian's mod that you might consider taking up. The Super Project and One/Planet production improvements *also* produce some of what they are boosting. E.g. Tech Capitol produced 12 RP as well as the bonus. Thus a lone RC wouldn't be an issue...
I don't know his mod, and it could be done, but the only way would then be to let this improvement have the maximum output (just like the Neutrality Center is designed) otherwise it will be placed also on bonustiles and that may be suboptimal if better labs become available.
I personally like all the research-boosting improvements, because they will also enhance production that comes via focus, ie. if you play a all-fac strat, or if you have a planet with alot of base industry output then building such an improvement there may be reasonable. Although, and especially at higher difficulty levels, the AI is usually better off by adding base RP/Ind to a planet, because he gets tremendous percentage increases to RP/Ind anyway from this setting....