I noticed that you only complain to my suggestions, so why don't you:
1. Stop assuming and putting words into my mouth (I'm ignoring you because you have made no valid alternatives to the things you were complaining about.)
2. Make a constructive suggestion just like Maupster did above.
First.
1. and 2. are saying the same thing, so you only have 1 point.
Second:
You want an in-game advantage for having the same players on a team for longer periods of time together. You want it in such a way that there are no apparent negative side-effects to it, and your suggestion for how it should be implemented benefits BOTs more than anyone...
So, rather than implementing it in your manner. Have the rate at which "experience" improves be less rigid and set in stone as X for league, y for cup, and Z for U21/NT games as ways to increase it.
and make those gains much smaller, but instead have hidden stats like aggressiveness, and clutch, for the chemistry, to where Player X gains experience A faster when playing with player Y, but when Player X is playing with Player Z, his experience gains A slower, because they have poorer chemistry.
This way you still get gains like you want, but, they are not just handed out and given to you like its entitled to you. You have to find the combinations to make it work better. Adds more challenge and fun.