Personally, I list fiddling with cohorts under the heading of "not worth stressing over." I'm sure that there are balance issues in the minutae, but I don't think it requires getting into too much of a bind. This is how cohorts are dealt with in the game that I play in (the cohort is mine) and how I would run them if one of my players wanted one.
XP: Refigure all the awards of CRs for the cohort's level (two levels behind the PC, if their leadership score is maxed out). Divide by everyone in the party, plus the cohort. He doesn't get a share of the group's XP, but he recieves awards for being a full contributor to the encounters. In this method, the cohort often gets as much or more XP than the party (since he's two levels behind), but since he can't be any higher level than his PCs level-2, it keeps things under control.
I play the cohort, and I keep his character sheet up to date. Does he often fall by the wayside? Yes. Frankly, though, it doesn't bother me or anyone else. I don't use him to hog more of the spotlight than I should have, and he speaks up when he has something to say.
Of course, my situation is a little bit different, because of the nature of my cohort. My druid found the mouse familiar of a dead wizard in a dungeon, and, since the wizard had been high enough level that the mouse had a reasonable intelligence score, my DM let me take the leadership feat so I could keep the mouse with me, and designed a "liberated familiar" template to make the mouse a character. Demitrius has levels in rogue and sorceror, and basically functions as the party lockpick. As such, it's easier on me and the party, because he doesn't have much of a reason to talk to anyone but me, and everyone else ignores the mouse unless they want him to do something. He also doesn't get a share of the treasure, but what can you do.
As far as NORMAL cohorts go, I think that the cohorts themselves do the balancing in the end. A lot of players have better things they'd rather spend that 6th level feat on. The encounters become more dangerous to everyone when the DM starts factoring in those cohorts in determining ELs. And normal cohorts need shares of the treasure to keep up, so that will keep too many people from wanting one. Besides, controling more than one person just gets to be a pain at times.
Unless it's a situation where the PC and the cohort are talking, I think the DM should not control the cohort. Turning the cohort into an NPC makes him a tool of the DM, and he should really be the tool of the player. If the PC is abusing his cohort, then it's time to step in. Otherwise, if the player really wants an adoring bard to play wish-fullfillment with....well...two man tents from the PHB don't cost that much.
