Would it help you to know that in the current beta, scientific leaders are now an option?
I hadn't heard of that yet. Checking CFC now, Tavis just posted about that right about the same time as Sirian posted his screed. That would seem to solve that issue.
As for armies, they really aren't any more unstoppable than they were in Civ3/PTW. The AI never attacks them in any version. It's just a question of speed; with the extra move and the fast healing, you can use them more often. And you do tend to get more armies, with that now being the always-do option for military GLs rather than rushing a wonder. I don't really see a problem with armies; whenever the player invades an AI civ with enough force, that civ is dead anyway; doesn't really matter if an army makes that happen slightly faster.
I'm still not convinced there's actually any change to AI Republic/Democracy behavior in C3C. The war weariness bug is not new; it's been there all along. And I've seen plenty times before AIs staying in representative governments until the end. The only real difference with AI governments is that they seem to always prefer Fascism over Communism or Monarchy.
As for runaway civs, there's a big factor that doesn't seem to have been publicized: it seems that there's no longer a discount for buying a tech as compared to researching it. Once a civ gets ahead in tech, it stays there - there's no discount to help catch up the trailers. The worst case is if a civ gets another to pay full monopoly price. This, IMO, is the real cause of AI tech runaway wins. (The corruption changes - higher base OCN, lower max corruption - contribute to this too. In older versions, the 20th through 30th cities that a civ might get would be economically useless, but now they can become significant economic producers.)