I find them pretty good actually.
I am just beginning my campaign with 6 Gestalt Characters in the group. I plan on only converting major NPC's to the Gestalt Rules. I used 32 non-standard point buy for the ability score generation. This really made a difference. I found that most of my players had to make some hard choices of where to put their good stats. True that they will be able to last a bit longer due to having more spells, but their DC's may not be as high. Most of the time you will be choosing a "Primary" class to favor with your stats and using the abilities of the second to support the primary. Also while you get a lot of class skills, you don't get enough points to act in 2 roles. (IE a Gestalt Rogue/Sorcerer gets more class skills than a Rogue, but still has the same amount of skill points.) Also feat choices are limited with any combination but a Gestalt Fighter/(Whatever).
I am only doing minor boosting to my campaign. Not every enemy will be a Gestalt character. So far it looks good.
Delkain