Floor slopes on the corners of walls
Particularly areas you kick or jump from. Doesn't anyone realise how annoying it is when you get stuck in a corner for a second, with no means of turning back, messing up your jump? To make the matter worse, on areas that require you to actually gain speed. It's not a huge pet peeve since it doesn't happen consistently, however (when running and jumping). Infact, getting stuck on a corner from kicking happens with Spaz (but I admit I don't mind it too much since he's the best MP character and I use him irreguarly).

Pin-point 1 tile floor holes
Basically 1 tile holes that aren't in corners, which require much percision and slowing down. You know why no one uses them in-game? Because they're stupidly risky and mess with the flow. I can guarantee 9 times out of 10 I try to use them, I'll get hurt by some projectile. Multiplayer is simply too fast paced to accomodate for pin-point platforming. I can forgive TRF for doing this because it would be too easy to rush scoring, however. Oh and the bases in WW are quite like this, resulting in players not capturing because of the way the bases are placed between slopes. For hells sake camel, put the new version up for already (which fixes this issue).

Single paths to important areas
For example, CTF bases. Even worse if the area can't be attacked without getting yourself hurt. "Oh but it's a strategy" you say, well, if you define "Strategy" by whoever reaches that point first to win. If there's no way to counter it, wheres the strategic depth? Are we supposed to play the same map the same damn way to have "fun"? This pertains a lot more to old levels (albeit widely accepted), however.

Carrots that are too close to each other in battle
That particularly applies to smaller games. But if you ever want to over-centralise a map, this is the way to do it. It's not too common, however.

And I didn't mention anything about character compatibility and character balance. Shock-horror! But that's because I think most modern levels are playable with all characters, however (and that I can accept copter ears suck - I imagine you'll be able to do something about that in later versions of JJ2+).