The main thing for me is the audio but I'm not sure if the ps3 is able to use all of the audio formats that are out right now. My reciever is able to but is the ps3 able to? Also does 40 gig 80 gig or 120 gig make any difference with the audio aswell.
Audio features is definitely the main place the PS3 fails in the blu-ray category compared to other options IMO.
Are you going to play games with it too?
-If so, this would be an option. If you aren't going to play games, I would get a stand alone player, no question.
Do you have an HDMI 1.3 compatible receiver?
-If not, I would go with a player that can decode audio internally and output it via analog 5.1 to your AVR's preamp inputs. The PS3 most certainly cannot do this. IMO, you should look at the Panasonic BD-55k or the Sony BD-S550 if this is the case.
Bottom line: if PS3 games aren't your top priority I don't think you should purchase a game console to play blu-rays. Depending on your HDMI situation, get one of the stand-alone Panasonics (my personal preference), Sonys, or the top-end Samsung (which can also stream netflix). If you have unlimited funds, you should also look at the Denon flagship player. Just my two cents.
As for your other question, there is no difference between the different hard drive sizes as far as blu-ray playback is concerned.
Hope this helps!!