@Senevri: If you're shying away from full Gestalt, I've seen several implementations of Partial Gestalt in action. The first instance was in Sinfire Titan's Fall of Sharn campaign, and worked by, if I remember correctly, allowing only
Tier 3 and lower classes to gestalt (aka, no gestalting Warmage with Wizard, or Crusader with Cleric, etc.) while Tier 1 and 2 can't Gestalt with anything but the lowest tier. Of course, if you believe in the Tier system as it is constructed.
Another, one that Amechra is using in the Monster campaign is gestalt only at every odd level, mostly due to everyone only taking monster classes on the main side.
One option could be to make it mandatory for the first one or a handful of gestalt levels on one side be used for some LA, and then limit the classes that can be used from then on. That might help keep us from achieving full spellcasting on two sides, for instance. Though, that could also be achieved via option 1, above.