I've experimented with this... I thought I was being creative at the time... didn't even know "gestalt" was an official concept! (that's what I get for still using 3.0 manuals and just cherry picking stuff from the 3.5 SRD)
We granted mutli-classers the best of their two classes hit dice, and it seemed to work out fine that way. Yes, the multi-classer is more advantaged initially, but it really begins to even out as the single classers pull ahead as they level up.
It may help to restrict certain class combinations, too.
It may be sort of perverse, but I've never been part of a group that was much interested in playing characters over 12th level. I'm aware, however, that the multi-class character really starts to eat it past a certain point in terms of having to divide experience.
Beyond any mechanical considersations, 3.x m-classing has ever bugged me in terms of story logic (something, I'm afraid, I'm a real stickler about...). The idea that someone just shows up one day with a level in a profession they have demonstrated no previous knowledge or skill in, is really absurd. It takes years of full time study/practice/training to become a first level character in any class, and some (particularly the wizard and monk) much more so than others. These studies and apprenticeships often cost money as well. Sometimes BIG money... at least in my campaigns. Saying you're just hanging out with some wizard in your off hours, or looking over Mialee's shoulder or whatever, doesn't wash with me.
True, dual-classing in AD&D posed the same sorts of questions. But, it was never an issue I had to deal with personally, 'cause no one ever wanted to go through that period of reverting back to 1st level and not being able to use their other classes' abilities, while all of their companions were leveling up. Also, the steep ability requisites often ruled out a fair number of characters from being able to dual class.