I'm torn between the manhattan project and longevity, as everyone else here has started to mention. I think nukes should just come with the tech that they need. No wonder, no small wonder. When you know someone has the tech, you know they can build nukes if they have the resources, as Ramalhao mentioned. There's no reason to have a small wonder because if you can build the nukes why waste your time with a small wonder. If I could make mods I would just eliminate the idea of a wonder, small, or big, proffering the prospect of nuclear war and leave it at a tech. I think having it as a big wonder is actually better than as a small wonder for the same reason but that's just me.
I don't think the colossus is too bad. I do agree you almost always have something better to build, but it gives some nice culture and ok money (don't forget it'll probably eventually be a tourist attraction if you have C3C) if you're forced to switch to it, which shouldn't happen very often.
I do hate the odd growth problem that is exacerbated by Longevity, and no one ever goes around building it my games, the AI is usually licking my boot while I tear down their infantry with modern armor. The game is usually over before I can even build it, for that matter. I'm going to vote for Longevity.