I use instrument tracks a lot and have only had one or two minor problems with them (that I can't even remember off hand so they can't have been that important).
First of all they're quicker to set up. Secondly, the only thing missing from them that I've noticed (and I've still never been able to work out why) is that the Audio part of them does not have a stereo/mono interleave button. But when I have to use that, I simply right click on the track, select "split instrument track," flick the interleave button, then select "create instrument track" to consolidate it again.
For me, the quick setup and the MUCH tidier appearance outweighs any disadvantages (which I've yet to encounter).