I've always seen it played in Pathfinder that favored classes are just treated as the rules say. Races can apply their race-specific favored class bonuses when they take a level in that class. This means that half-elves can benefit from favored class bonuses from both sides of the gestalt at the same time.
... just a perk of being half-elf.
I'd say:
A gestalt half-elf taking both favoured classes can choose which one to apply the level bonus to, but not both, effectively making a choice between:
+1 hp
+1 skill rank
Left side class bonus
Right side class bonus
But choose only one.
As for mythic, mythic paths aren't classes - so mythic gestalts should choose ONE path.
Ok. If you aren't a half-elf, and don't somehow have an extra favoured class from another source, you still have one favoured class. As such, when you gestalt it to another, you can take either +1 hp, +1 skill rank, or the class bonus that applies to your favoured class.
If you take the class bonus, you apply it to your FC's mechanics as though you weren't gestalt. This could result in applying to a shared mechanic (eg, it applies to a bonus to CMB or CMD,) or one unique to the class (eg, a sorcerer's extra spell known.)
I would follow the same general Gestalt rule of look at what you gain on both sides and take the best. So if you get +1 Base Attack on one side and +0 Base Attack on the other, you get +1. If it is +1 on both sides, you still only get +1.
So a Half-Elf with both favored classes, you would still only get the bonus from one of them, since favored bonus wouldn't "stack". You only get one per level (though Half-Elves can choose which one to take if both of their classes are favored).
At least that's how we run it.
What "best progression" means has been table-variable ever since the gestalt rules were written. Consider a fighter 1 / ranger 19 gestalted with monk 20.
Would the saves be:
+12 Fort, +12 Ref, +12 Will
"You took 20 levels in which all three saves were good."
+23 Fort, +23 Ref, +15 Will
"If either class gives a plus at its class level, the gestalt gets a plus."
You'll see people make arguments for either of these, and sometimes others as well.
humm i always thoguht the attack bonus and saving trhow was not the best attack at the lvl but the best attack/saving progression :P
Correct. What I meant was if you were Gestalt Fighter / Barbarian for the full 20 levels, at each level your Base Attack goes up 1. If you were a Fighter / Wizard for the full 20 levels, your Base Attack would be the same as the Fighter / Barbarian since you only take the better of the two sides (at any given level).
Fighter / Wizard level 8 = +8 Base Attack, +6 Fort, +2 Reflex, +6 Will
If both of those happen to be your favored class, you get 8 levels worth of Favored Class bonus. Either from Fighter or Wizard (could have 4 from Fighter and 4 from Wizard or any combo of 8).
For me it is easiest to track Gestalt level progression on a spreadsheet so you can see exactly what you get at every level. Of course I almost always just go all 20 levels in the two classes I choose which makes the level progression chart super easy.
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Allowing two mythic paths results in insanely powerful characters. Do not attempt unless as the GM you plan on spending a crazy amount of time on prep work trying to figure out and build foes to challenge your PCs.
If you're asking as a player, I'd say no if you asked and I was your GM.
Ask your GM what his opinion is on it.