Here is my thinking on skills and please excuse if someone has already suggested this as I haven't finished reading this whole thread.
Use the 3.5 system for skills with the revised skill list in alpha but remove class vs. cross class skills. All skills can be taken by all classes. What makes rogues so great at skills is the number of skill points they get over other classes. If we can agree that some skills like Disable device/open lock (yes I think those should go together) should be rogue skills we impose a feat requirement that a rogue gets as a function of thier class. This works much like Tracking.
For example anyone can take Disable device but to use it on any trap with a DC higher than 10 you need the feat Trap disarming.
Now if your fighter wants to use a feat to be able to disarm traps he can but he has less skill points so he is sacrificing something else to do it along with a feat which makes him a less capable fighter for diverting his attention from his profession.
As for DM's, well some DM's like statting up all of thier NPC's some don't. This screams optional rule. Perhaps something along the lines of a skill pool.
For example lets say you roll up an NPC that is just for a quick fight and you don't want to do all his skills. We take his skill total and create a skill pool. Lets say he has 100 skill points available. You set that aside. You run your combat and say you need to make a ride check, you make a quick decision based on how good you think he is at that skill (sounds random but as a DM your the only one who can answer that question) and subtract the number of ranks you grant him from his skill pool. Jot it down in case he survives and you reuse him later. If for some reason best flute player comes up in battle well apply the same logic as above. Anhy major NPC you'd probably want to stat up completely which actually won't be that bad since we dropped class/cross class skils which is the most agrivating part of skills.
Now we go back to humans and half elves and change that make a class skill ability to extra skill points for humans. You could do the same for half elves but personally I think the half elves and humans are still to similar. I'd change half elves to +2 to any, +2 to any, (cannot choose the same ability) and -2 to any.
This gives the customization many if not all players are looking for while reducing prep time for DM's. It is simple and easy in my humble opinion. I never really understood why Class skills was needed. Why on earth can't you have a perceptive fighter or a mage who can lie through his teeth just as good as any rogue. Again if a skill like spellcraft is needed to be separate use the feat system to seperate it out and give it as a free feat to the class you want to have it.
for example
Student of spells- without this feat your max rank in spellcraft can never exceed half your character level.
That is just my two cents from my limited gaming experience of 2nd edition on up plus whatever else I can get my hands on.