There is a training camp type area on ps3, but I've never seen or done them for franchise, just as a separate game. I dont remember seeing where you could run a player through a drill to boost his stats like the ps2. The minigames on the ps3 have bench press and 40 yrd dash (which a very dull imo) and ps2 had the swat ball, and a few others that were a lot more fun to me.
Franchise on ps2 has better progression, stats and I dont think there was a problem with keeping players lost for the season. I've never gotten past week 6 of a franchise on ps3, I have heard that if players are lost for the season you can't replace them without dropping the injured guy.
Yes, there are gameplay issues as far as blocking, pursuit angles, defenders and wrs get superhuman speed bursts to the ball at times. Precision passing isn't as variable as ps2 either and you lose some defensive adjustments like individually playing off or bumping certain wrs and shading to the inside or outside of wrs.
It's tough call. If you get a chance try the game or demo out first. Right now for me I feel like the guy they took out of the matrix. I've made the leap from ps2 to ps3 and now I can't go back cause of hd graphics. Man, ignorance was bliss.