I also have both FIFA and PES (both bought on release of PES), after playing PES initially I switched to FIFA mainly for 10 v 10 and switched the controls to manual, after a few weeks went back to PES the manual stick (IMO) is far better than the controls in FIFA, I use the stick for every thing, the only down side to this is that shots on goal are still classed as passes therefore are not shown in the stats, don't initiate a replay (unless you it the woodwork) and more importantly if you have a player in an offside position when shooting the ref will blow up, scored a great lob when the keeper threw it out from the edge of his box and I intercepted and lobbed him running back, only for my SMF to be stood in an offside position not 2m from the corner flag.
In terms of tricks, for a little while I thought that FIFA had it right with the way they have implemented it, however watching PES more closely and noticing the subtle faints and little things that you can do when quckly flicking the controls are excellent, so I think that PES have the upper hand there too.