Only two big things I can think of at the moment concerning wonders.
1. No wonders like Leonardo's Workshop or JS Bach's Cathedral. I know they were a big part of the old series, but after the introduction of Great People in Civ4, I think it's proper that they aren't necessary. Some may disagree on this with me, of course...
I agree whole-heartedly there. Especially because they don't really represent anything substantive. I'm iffy about things like Rock and Roll as well. I realize it was an effort to expand luxuries, but it doesn't really make sense as something built.
I'd argue that the goals should be two fold. One is increased world diversity, the second is increased age balance. I realize that the bulk of wonders in popular mindset are ancient, but there needs to be things to be built throughout the game.
Ironically, I'd still argue for including the 7 Ancient Wonders even if this seems to directly contradict what I just said (they're all Greek with the exception of two Middle Eastern ones and they're all ancient). But, after that, things can be reevaluated (like replacing the Hoover Dam with the 3 Gorges Dam was a good idea).
Anyway, I'll echo people who said the Large Hadron Collider. It fits perfectly with the goals above.
Less fitting would be the Terra Cotta Army. I've been pushing to have it replace Leonardo's Workshop for a long time and I think it would make sense. Plus, it brings world culture instead of simply western. The Grand Canal from China is another that comes to mind, but I don't think it should be the Greece and China show either (plus, you don't want too many ancient).
One thing that is truly a wonder would be the Petra in Jordan. Sure there are other Middle Eastern wonders and it's also ancient, but it is simply amazing and deserves consideration. As for the Colosseum: If they keep small wonders, I think it would be an appropriate one (with amphitheaters replacing the generic Colosseum). It certainly is awesome, but, compared to some other ancient ones, falls a tad bit short.
As far as removing wonders. Definitely 86 Rock and Roll, Broadway, and Hollywood. Aside from that, everything seems cool unless it interferes with balance by being too top heavy.
Entirely different, but I'd love a completely revamped space race that would start with satellites and advance to manned missions, moon missions, space stations, and a trip to alpha centauri. I'm not sure if anyone would be willing to play that, but if it gave bonuses along the way to science, technology, and/or culture, people might be willing to try it. Plus, the space race would be more real than a parts race on one ship (with announced progress made by other civs when they hit a certain milestone).