AbdulAlhazred
Legend
Haven't read the rest so if I'm repeating - sorry.
The difference between attacks and skills is +5.
With skills if you are trained you get +5 to that skill.
Your attacks/defences do not get +5 for being trained.
All you need to do is add +5 to the defences when opposing a skill.
If you are rolling Acrobatics Vs Reflex just add +5 to Reflex.
Really if you were to create the system from scratch you would have
Defences +10 (take 10) +5 (training) +(1/2 level) +abil
Attack +D20 +5 (training) + (1/2 level) +abil
((SkillCheck +D20 +5 (training) + (1/2 level) +abil))
(You could even have PCs roll attacks for things they are not trained in such as other classes powers but without the +5)
As for DCs part of that, don't ask me, I imagine DCs should be comparable to enemy Defences.
Oh, there are various ways to make a d20 skill system that would work out better than the 4e one does in terms of consistency. The problem is attacks have to factor in enhancement bonus and skills have to factor in ability score increases that only some get. Then add in items that improve skills and other factors and it gets a bit trickier.
The upshot is if you started over clean slate and wrote a game very similar to 4e you could make skills work better. There's just no way to retro-fit it into the existing system without changing the numbers for practically everything.
I think the fundamental issue is they designed the combat system first, made level scaling work with that, and then did the skill system. That was backwards. As you are essentially noting, combat is a skill and thus the skill system should be the more general case and combat the more specific sub-case. If games were designed in a linear ground-up fashion from scratch that probably would have happened, but 4e evolved in stages from 3.5/d20. It works pretty well nevertheless.