I haven't done any serious recording, so my opinion here probably doesn't count for much, but it's still fun to jump in..
I think that for me it would boil down to this :
You can't get the "feel" of a real amp turned up and moving air and you actually feeling the vibration in your hands and through your body. And that feel carries over into how I play and how the guitar reacts, sustains, etc. It would take a nice big powerful monitroing system to run an amp sim through to aproach that experience.
But recording a real amp with never give you the control over your tone that an amp sim does after the fact and in the mix of a recording.
So the best scenerio would be to use both as some have suggested some of the pros are now doing.
But for many of us, recording a real amp cranked up at home is not always possible or at least practicle. I have ended up with some guitar tracks going direct with my old Yamaha DG Stomp (digital modeler) that I was very happy with. And I expect to get even better results with the Guitar Combos package I just bought (and have still not found time to install and play with!!!).