We are currently playing a gestalt campaign and while the character creation is a lot more complicated, its nice to be a well rounded yet powerful character. As 4 lvl 3s, a CR4 still almost killed a party member, and a CR5 takes a lot of planning to avoid death.
Our current rules allow prestige and multiclassing. this is the second game for gestalt for me, and the 4th or 5th for the rest of the group. But our rules state that the 2 sides of gestalt are seperate. That is the class abilities of one side do not effect the other. So if you were a wu jen with fire mastery, your wizard on the other side would not gain the caster level increase. With this requirement we also made that to qualify for prestige, that one side must qualify. So the wizard//wu jen must seperatly qualify for, say archmage, if both sides want archmage. And lastly, he uses this rule sparingly, but the same class ability on both sides does not stack. So if both sides were fighter, you dont gain x2 fighter feats. Same idea with rogue and evasion, in that you dont get improved evasion because you went rogue//rogue.
while you can make overpowered characters, the biggest benefit is you dont have a wizard who cant do anything because he either ran out of spells, or doesnt want to waste it incase a bigger thing comes. Or you end up with a fighter who is great with sword and bow. A ninja rogue makes a really mean sneak attacker. And the warlock is highly beneficial.
i agree with those of you who said to make one side your "primary", and the other just compliment it. I play a dread necro//warlock, and use the warlock as a boost to the dread necro, as the warlock has some great 24hr spells. (Can you say +6 bluff, +6 diplomacy, and +6 Intimidate, for 24hrs, thank you very much. Very handy to "I am not the necromancer you are looking for", or "What zombie, oh him, no hes my brother, and hes just a little slow...") Plus the warlocks eldritch blast is a nice attack without me wasting spells or being in melee.