2) You're getting substituted near the end of matches because your stamina is too low.. and you want to end it.. isn't it obvious what you should do? Conserve your stamina! Run only when you need to and move as little as possible. Don't go running around chasing the ball
3) First thing I would like to point out is that you should not distribute strengthening points to all stats. I think it's better if you concentrate on 2 or 3 stats at a given time. On the other hand, yes. As you grow older your stats grow slower. Get a place in your national team, play in the Champions League etc to gain more match exp.
2) Well, currently my stamina is improving to the point where I don't get substituted each game. That also has to do with the fact Real Madrid bought me and these guys have more possession which leaves me in better position to receive a good deal of passes instead of actually fetching the ball at the other end of the pitch, which I was forced to do when I played at lesser teams if I wanted to be "important" for my team.
3) I guess I made a mistake by going for averaging my Strengthen points. Too late now, however. Maybe I'll start over at Top Player or Professional, and select more adequate Strengthen points.
Two other things that I noticed:
1) I got bought two times by really big teams that were, at the moment, "out of my league". First from Sparta Rotterdam to PSV (19 y/a), and then from PSV to Real Madrid (20). Actually I played against both teams and played very good games, scoring and assisting against PSV and Real Madrid. So maybe good performance makes your opponents want to buy you?
2) Both at PSV and Real Madrid I felt like playing at freakin' relegation teams. Your team is never really in control of a game, and if you win, it's always close. It's also no coincidence that during my four seasons my team always ended up getting mostly draws, far more than wins and losses. This leaves me wondering that chance is a way bigger factor than actual quality in deciding the fate of a game, which means the AI is truly shit. Follow me? Also, your team always scores and concedes fewer goals than the rest of the league, and way too many goals are from corner kicks and rebounds, which more or less embody chance. Conclusion: PES still sucks when playing against CPU. Unfortunately I moved out of my student dorm and now I have no mates to play with...

Anyways, I hope restarting my game at Professional/Top Player will improve team AI, cuz at the moment I'm too bugged by my teammates at Real Madrid to continue BAL. It's like: everytime I serve them the ball on a plate, they miss, and and each time they should pass it to me, they horribly fail at trying to score themselves. And I'm talking Van Nistelrooys and Rauls. Now don't tell me you don't hate that.