My angle on this is as a GM, first with one player (3 different campaigns), and another time with 2 players (1 campaign).
The bulk of balancing the game will be on the GM's shoulders. An NPC is possibly his best asset for helping the PCs through difficult encounters. Don't leave home without one!
The real restriction that still exists for the players is the action economy. You still get only a full-round action, even though you might have access to 2 full classes worth of abilities. This becomes a real choke-point as soon as one of the PCs goes unconscious, and then the burden shifts solely onto the remaining PC. This is the real danger zone of a small party, gestalt or otherwise.
Keeping that in mind, I would HIGHLY recommend you allow an NPC to tag along. He can remain in the background 90% of the time, but that last 10% could be him pulling one of you to safety and giving you a potion of healing while the other PC tries to finish the fight. Are you going to want to disengage to heal your partner when he falls in battle, and possibly give free attacks to your potentially multiple enemies? Bad idea--or at least, not a very healthy one.
I won't speak to the ECL, because as GM, I found myself considering much more closely how my players would naturally react to all my encounters. I was very careful to adjust mob sizes, by tempering them with morale checks if I felt my mob was too big. Or essentially treating them as 2 hp mooks, and softening up the PCs just enough before revealing a bigger, stronger, boss-type creature to carry the "meat" of the encounter.
Before choosing classes, ask the GM if he is willing to customize how healing works. This is essential if you don't choose a healing class, and you don't want to spend a week in bedrest after every combat. I allowed a modified healing skill, which acted as a cure spell once per day, and later twice per day. And I think I used one type of healing potion which always healed half of an individuals total HP. (Because if you spend a round drinking a weak healing potion, and then get hit for that same amount next round, you didn't gain anything really and should have just kept fighting instead to begin with.)
The GM will find it much easier to overwhelm you with mobs. Be prepared to be flanked, a lot. Even if they are mooks, those flanking bonuses multiplied by the number of mooks can add up to serious damage really fast.
Also, keep in mind that if you don't both melee, you likely give up any possibility of flanking, as mobs can quickly surround both of you. Animal companions can definitely help you out with this.