Gestalting works great for just a couple of characters, and can be fun even for a group up to four or so. (More people would probably be less fun, as you'd have too much overlap between individual PC's abilities.)
Gestalt characters have more flexibility at any given moment. However, you shouold expect that your gestalt character will be slightly less good at specific class-based things than a single-class character. For example, your skill points and feats have to be selected to support both of your classes, so you might not be able to get all the feats you think you need. Likewise, your magic items will be divided between things to support both character classes.
We've done a couple of different gestalt campaigns, one with four characters, the other with just two. Especially if you'll have just two characters, I recommend increasing the rate at which feats are gained (maybe one every 2 levels instead of every 3), and increasing the money each character has at a given level.
On the other hand, you'll generally be fighting creatures that are a couple CR higher than you otherwise would. When determining XPs gained each session, I recommend subtracting one or two from your character level, and one or two from the CR of the critters you fight, to keep from leveling up to quickly. (Determining whether one or two works best requires experimentation and your group's decision on how fast you want to level up.)