It seems as though the general progression of the governments is:
expansion/military conquest -> culture/happiness or empire building -> growth/ peacetime bonus -> production boom and/or intense war combat -> wealth building -> scientific specialization or general peacetime bonus -> general growth bonuses.
If that's right, then I think that there are a few sub policies that could be better optimized in a different government. Note: I have never played CTP so I don't know how each of the governments played out. Also, I didn't think about the position of the policies on the trees, so some of the better ones might be towards the top. I'll leave it up to you to decide where to put the bonuses, assuming you decide to add some. None of these changes I have proposed are what I would consider "high priority;" I am pretty content with the way they are now, but if I had to change somethings, here is what I would do:
I'm pretty happy with Monarchy as it is now; the only change I would make would be to change the great person bonus from Dynasty to a bonus to strategic resources. It keeps it more in line with military conquest.
In Republic, I would take out the discount for buying units. In it's place, I would give a bonus to Great People spawn rates. I would also switch its Rule of Law bonus with Theocracy's Religious Law. Republic is the empire building government, so it should get the reduced building maintenance, while the cultural government Theocracy should get border expansions faster.
The Discipline sub policy for Fascism doesn't help much in the area of conquest. I think something that lowers unhappiness for occupied cities would go better with the whole "kick 'butt' and take names later" theme. It allows the player to keep chugging without worrying too much about happiness issues. The garrison helps as well; it's like you are telling your citizens "we are gonna fight and you're gonna be happy about it

."
If Communism came by itself I wouldn't have a problem with the way it is. However, since it comes at the same time as Fascism, I think it should
not be a military government. To that extent, Comitern sort of clashes with Fascism, as now you have two ways to wage war, the super elite killing force or the industrial powerhouse. Actually, now that I think about it, that doesn't sound like a bad idea. I would probably lower the Great General rate and/or the unit maintenance to distinguish it further. I would kind of like to see a bonus towards buildings in the sub-policies, perhaps where Comitern was. Either way is good.
Corporate is great the way it is. I see it as the economic recovery after the war. One minor thing that could be changed is the Shareholder View, which halves unhappiness from specialist. I was thinking something like having luxury resources and/or happiness buildings be slightly (10-20%) more effective. This would be in line with the general uplifted spirits when embracing an economic boom. It would also help soften the loss of the garrisons.
**Note: The Digital governments are probably going to be the most unbalanced of them all. I was just thinking of useful things that could be implemented, with little regard to how it balances with the rest of the mod, including other governments. I guess these should just be considered as broad strokes toward an ideal.**
The Digital Era comes with two governments, one which specializes in science, the other focusing on growth. Therefore, I really don't understand the reason for the policies that improve strategic resources. If anything, I think these should go to the Industrial Era governments, 100% to Fascism, 50% to Communism. Also, I think the production bonus that are granted when adopting Technocracy should be switched with the ones on Ecotopia. I think of Ecotopia as an empire building government, so the extra production makes sense. For that same reason, I would move Energy Accounting's building bonus to Ecotopia. In its place, I would make a policy that gives a certain amount of science to improvements and possibly ocean tiles (to simulate deep-sea exploration). At the same time, I would lower the gold generation of Ecotopia to 10-15%, and increase the gold for Technocracy to 25-30%. The reasoning: scientific enhancements usually come with economic prosperity. In keeping with the science/specialist feel of Technocracy, I would bring over the effects of Fascism's Discipline (specialist only consume 1/2 food) which would switch with the quantity resources increase. Finally, I woud change the benefit of Eco Fanaticism to something else, maybe happiness for jungle/forest. The bonus to unit movement cost seem like a war-type bonus, but it's probably too advanced for some of the Industrial techs.
Virtual Democracy seems good as it is in its role of end-game government. It's a little iffy, but I feel like the science should be lowered a little so it doesn't completely beat out Technocracy, especially since it only comes one era later.
It would be nice to see a war government for the late game as well.