Here's what I do with skills in my home campaign that might work for Pathfinder.
Skills have three tiers:
Untrained = 0 ranks
Cross-trained = (HD + 3)/2 ranks
Trained = HD + 3 ranks
All skills start as untrained.
When you take a class, all skills on their skill list become cross-trained.
Every level, instead of gaining skill ranks, you train in a single skill; untrained to cross-trained or cross-trained to trained.
If you multiclass and the new class gives you a cross-trained skill you've already taken cross-training in, it upgrades to trained; if you're already trained, pick a new skill to train in.
Corner-case stuff:
Humans gain training in an extra skill at first level.
Cross-training in a language allows you to speak and read it.
Barbarians can learn to read and write by cross-training in literacy.
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It's easy to keep track of. For each skill, add up your ability modifiers, racial modifiers, etc. (you're already doing it now, so nothing new here). Add a note of what training level it's at ("U"ntrained, "C"ross-trained, or "T"rained). Keep a note at the top of the skill section on your character sheet showing what your trained and cross-trained bonuses are. Then if you need to roll a skill check simply add your training bonus to your total modifiers and you're done.
No more changes to a half-dozen or more skill totals every level. Your base additions are what you calculate, and you add a set number to that depending on your training level. Going up a level with regards to skills is as simple as changing a U to a C or a C to a T and changing two numbers at the top of your skill section.
As for backwards compatibility, most monsters have max ranks for their skills in their stat block, which this system duplicates as training, so you've got the same numbers. And since most monsters barely even use their skills during combat it doesn't really affect using them on the fly, but if you wanted to it's easy. If it's in their stat block it's a cross-trained skill (equivalent to how skills listed in a stat block are class skills in 3.5), so they can be trained in a number of those skills equal to their HD. Lower the ranks in the rest to cross-trained and you're done.
been said by jason the alpha 2 skill system is firm not gonna br rewrote...might be tweeted a bit though