Instead of getting tougher, I thought it might make more sense to be able to pick up special abilities that build upon your favored class.

Since hit points don't change with this as a replacement and you still have to blow a feat, it is actually more backwards compatible.
When adjusting NPCs because of the increased feats for Pathfinder, the DM can just add favored class feats if the NPC has levels in its favored class instead looking over all the available feats. Therefore this could actually save time in adapting 3.5 campaigns to Pathfinder rules.

For example:

Blood Rage [FAVORED CLASS]
"You have drawn out greater rage from within."
Prerequisites: Barbarian level 1st
Benefits: You gain 2 additional rage points per day and 1 additional rage power of your choice. Whenever you are at 1/4 hit points or less, your bonus to Strength and Constitution while in a rage is 2 points higher and your morale bonus to Will saves is 1 point higher.

Arcane Prodigy [FAVORED CLASS]
"Your natural aptitude for magic improves your ability to wield magic."
Prerequisites: Arcane spellcaster class level 1st
Benefits: You gain a +1 bonus to effective caster level when you use arcane spells and spell-like abilities.

My thought on this has always been to add Racial Feats to the game that support both the race's characteristics as well as those of its favored class(es). I think using Racial Paragon Levels from UA as a starting point for Racial Feats design would work pretty well, and added some first passes on that in the Alpha 1 Racial Feats thread.

With the revision in races to support two favored classes, you'd need a good handful of feats for each race to support both options, but for me this is the winner as you make it entirely optional how (or even if) the concept of "favored class" applies to any individual character. I'm not completely sold on the +1 hp per level, though if we simply must have something automatic for favored classes I prefer a bonus to a penalty.

I like +1 Skill Point per level. This adds to character abilities, but doesn't make them tougher. It also scales nicely with the number of levels they take in the class.

A bonus feat tied to each class would be a lot of extra rules text that probably isn't necessary and would be hard to balance.

I like the +1HP/Level because it is elegant. I just don't picture an elf wizard being tougher because he's a wizard.

In my home games, I like to use the Gestalt rules for favored classes (from Unearthed Arcana). At first level, you get the abilities of your favored class in addition to another class that you select. If an elf wants to be a wizard, he can choose Wiz/Ftr at first level, and then Wiz every level after that. If he wants to be a fighter, he has Wiz/Ftr at first level, allowing him to dabble in the arcane no matter what he chooses later. Thus, all elves can cast spells, all half-orcs start with Rage and d12 HD, all halflings have good skills and Sneak Attack, and all humans are very versatile in some other way.

-Scotto

The main advantage of one hp per level or one skill rank per level is scaling. The advantage the character gains from joining a favored class is directly dependent on the number of levels he takes in that class.
Concering the point of backward compatibility, half the classes already changed their hit die in pathfinder, so even without the modification from favored class, there are lots of change in that area.
Special racial feats would be nice, but I'd rather see them in addition to the other benefits of taking levels in a favored class. That way, they could be tailored to class and allow some differentiation of races with the same favored class. It would also reduce the necessity of making them better than normal feats, an endeavor that all to often results in disaster.

Concering the point of backward compatibility, half the classes already changed their hit die in pathfinder, so even without the modification from favored class, there are lots of change in that area.

I think that changing the hit dice for classes would have been unnecessary if they settled on more starting hit points at starting level. At higher levels it's easier to compensate for low hit points with the right feat choices, magic buffs, and magic items.

Sorry but I like the idea of ether a select or specific skill added to skill list or an additional skill rank each level. I think it is a sense-able bonus for what a favored class is supposed to to be.

I like +1 Skill Point per level. This adds to character abilities, but doesn't make them tougher. It also scales nicely with the number of levels they take in the class.

A bonus feat tied to each class would be a lot of extra rules text that probably isn't necessary and would be hard to balance. [...]

I agree, although 1 skill point wouldn't be bad either. Feats just seem like too much.

I like +1 Skill Point per level. This adds to character abilities, but doesn't make them tougher. It also scales nicely with the number of levels they take in the class.

-Scotto

Definitely, my vote

I think Pathfinder characters already gain enough hp bonuses (Weak/Standard/Hardy racial bonuses at 1st level, Wiz/Sor gain d6s, Rog gain d8s etc).

I like +1 skill point per level - and might help to quell those complaining about classes with only 2 + Int skills per level.

I do like the idea of Feats for favoured race/class combos, though it isn't very scalable, as races/classes beyond the core ones would miss out.

In my home games, I like to use the Gestalt rules for favored classes (from Unearthed Arcana). At first level, you get the abilities of your favored class in addition to another class that you select. If an elf wants to be a wizard, he can choose Wiz/Ftr at first level, and then Wiz every level after that. If he wants to be a fighter, he has Wiz/Ftr at first level, allowing him to dabble in the arcane no matter what he chooses later. Thus, all elves can cast spells, all half-orcs start with Rage and d12 HD, all halflings have good skills and Sneak Attack, and all humans are very versatile in some other way.

-Scotto

A very interesting concept ideed! It has the favoured class feel (at perhaps the expense of strengthening stereotypes), gives 1st level characters a few more tricks up their sleeve, with the benefit of improving 1st level survivability.