The changes I would make:
1) The easiest and one that would make a big difference, is to let the players be assisted by the physios without having to stop play (like they do in rugby), I'm sure the diving and faking would decrease dramatically.
2) Get rid of linesmen and let offsides and goals like the one in the Germany/England match be determined by the technology.
How would this work? Having a guy or two in a booth watching the game (with the help of the technology) and telling the ref in the pitch what to call. You may have to wait a little longer to make the calls but 99% of the time you'll get the right one.
A "challenge" (like in the NFL) wouldn't work in football 'cause even though it does work in a case where a goal in offside is allowed, 'cause all you have to do is to get back and annul the play, what happens if somebody that is onside is called for an offside and the play is stopped. That's just as unfair, and there's no way to get back from that. That's why I think the best thing is to just let the play proceed and be stopped only when the refs in the booth see an irregularity thanks to the help of the technology.
This method has a flaw though, a lot of goals will be scored and celebrations be made in vain.