Two things....
1. You can actually change the buttons around, but not physically, you go into settings and go to NEW instead of CLASSIC, this will give you the PES buttons but you still have to use the likes of R2 for run, which actually seems better since i tried to go back and play PES there recently(and had to revert to R1)
2. 09 is WAY differant then 08, it looks the same when everything is still but when things get moving it feels more like PES, pace has increased an awful lot, and then there's all the new things like collisons etc... which make the experience more authentic. The ball moves more realistically, i was hitting shots in the arena and you could see the flight of the ball take off and rise like a real ball would.
Also FIFA 09 is the first game to get peno's right, however 08 could'nt have got them more wrong.
In 08 when the power bar was increasing you would just move the goalie to the side you wanted to go for the save and if you guessed right the ball never went in, in 09 you can only move him a tiny bit and the ball goes to differant areas unlike other football sims which has the 6 usual directions(top right, bottom right etc...), i even hit one down the middle and instead of it going dead middle like it does in all games it curled with the players foot(i'd assume the keepers leg can get them like it nearly did when i put it down the middle, only had one shoot out)
I remember reading a few months ago that rumours were rife' that this FIFA was going to be the biz and from what i've played it is, PES has a lot of ground to make up if i'm going to be still calling myself a PES man this year