You gotta remember that everyone else that you are playing against (assuming you are playing online) is using the joystick too. It's definitely easier to aim with a mouse, but unfortunately in an FPS on consoles, you gotta stick with the joystick.
I haven't done extensive console FPS gaming, (not near the amount of PC FPS gaming I have done), but you will pick up different techniques along the way that you never knew in PC gaming. You will eventually get used to it, as long as you primarily play FPS on consoles.
Another option would be to play FPS on PC, and play all the other kinds of games (assuming you play other genres) on the PS3. I maintain that FPS will always be better on PC, however, I've never seen a good sports game made for the PC, among other genres.
As for PS3 vs Blu-ray, I'd suggest getting the PS3. To my knowledge, the PS3 isn't all that much more expensive than a decent Blu-ray player, but you'll be getting so much more with the PS3.