Disclaimer: I haven't been at my computer recently and just started looking at the rules. I haven't read the stuff elsewhere, so this may be redundant. If so I apologize.
Just a few comments and suggestions. I haven't playtested, these are just the initial impressions of a longtime 3.5 DM who had been fiddling with the rules on his own.
I had to read through the skill rules a couple times to follow what was going on. Maybe clean up the text a bit to make it easier to follow. Or maybe I'm just dense, which is a distinct possibility.
I love getting rid of skill points, I was doing something similar to Saga myself.
But one thing I was considering was a way to allow characters to get high bonuses to skills that are not "class skills". I just have a belief that if someone wants to learn about Magic, if they study it enough they can be as proficient as a wizard. Also, I was wondering if there was a way to make it a bit more multiclassing friendly. My litmus test is "fighter multiclassing into a rogue". You have to be able to go from fighter to rogue and gain proficiency in enough skills to be able to effectively find and disable traps, and maybe one other roguish like skill (use magic device, etc).
What if you did something like these mechanics. Bear with me, I learned in RPGSuperstar I am not a designer. These are similar to my house rules I have been playing with, but a little De-SAGAfied. In my gmaes I use the whole 1/2 Level +5 thing from SAGA, but I removed that from the above to help comply with the idea of backwards compatibility.
The check for trained skills is 1d20+Character Level+3+Ability Mod+Racial Mod.
The check for un-trained skills is 1d20+1/2*(Character Level+3)+Ability Mod+Racial Mod. Some skills may not be used untrained.
There is no such thing as "cross-class".
A character first chooses a number of trained skills equal to their intelligence bonus. These can be any skills from the full list of skills.
A character then chooses a number of additional trained skills based on their class. Barbarian chooses 4, Bard chooses 6, etc. These skills can only be chosen from the class skill list.
Miscellaneous stuff:
If a character's intelligence bonus increases via a permanent increase (inherent bonus, ability increase from higher level), they may choose another trained skill from the full list of skills.
I have ignored intelligence penalties, but if you wanted to include them just say that the intelligence penalty is added to the number of trained skills based on class.
Humans choose a bonus trained skill from the full list of skills.
When Multiclassing, choose a number of additional trained skills based on the new class. This number is equal to the starting skill number of that class divided by 2. So if multiclassing into Barbarian choose 2, if multiclassing into bard choose 3, etc. These skills can only be selected from the class skill list of the new class.
Prestige classes work like multiclassing.
Please utilize any, all, or none of this as you like. I am not saying it's perfect, and it definitely makes characters more powerful than their 3.5 counterparts, but that is something I decided fo allow for the same reasons they did it in SAGA.
Enjoy. If you have any questions I'll try to respond, but it may be intermittent during easter break.