It's pretty common to see a top WR in the slot now...whether or not it's a majority of the time or not is moot. If you're in man coverage, your #1 CB will NOT line up on the slot receiver.
I don't think you'll ever see a Champ Bailey or Revis line up as the nickle back in real life, either...no matter who is lined up in the slot, even if it's man coverage. I could be wrong there, but I've never seen it.
Few things I do that help (note: I don't play online, just CCM, and I don't do gameflow on defense ever....can cause matchup nightmares).
If you're in a
zone...you have to make sure your nickel back is lined up correctly. If the offense comes out in a typical 3 WR set, the slot receiver is on the left of the QB...and that's where the default nickel schemes line up your back. If the slot receiver is on the opposite side, audible and reverse your formation, which will line the nickel up on the other side. I also generally do press coverage on the slot receiver, even in a zone...even though it doesn't always make them press, it moves them closer to the receiver.
As has been said, you can "highlight" the receiver for your defense to focus on them...but this can get you beat pretty handily by other receivers.
Here's a pretty good write up of how to "hot route" your defense, but I personally still use the d-pad as I don't tend to miss with the defense too much:
http://www.madden-school.com/forum/m...beginners.html