Yeah, wheel routes suck. They sucked in 2k4 too. The problem, I think, is that the quarterback's dropback is way too short for the wheel route to develop. (Conversely, it might be that the wheel route takes way too long to develop.) Either way, though, you have to wait until the receiver/back running the wheel route turns the corner, like you noticed. Depending on the agility ratings of the route runner, you can be forced to wait a full two seconds to throw after the quarterback finishes his dropback just to ensure a complete pass. By that point, defenders are usually in position to tackle the guy as soon as he catches the ball.
There are a few other routes like this - ones where the spot that the quarterback is throwing the ball isn't really the spot where the player is likely to be. The wheel route is the worst, but shallow crossing routes can do the same thing. I don't have the game handy right now, but it seems like in many plays where tight ends run really shallow (2-3 yard) drags, the spot that the quarterback throws the ball toward is several yards in front of the receiver. You can sort of correct for these problems with maximum passing, but it requires an incredibly light touch of the analog stick in the opposite direction - one I can't reliably produce during an actual game even after practicing. I just try not to throw the ball to those players.