Personally I prefer something closer to the 3.5 system with a few additions, namely getting rid of cross-class cost and increasing skill points across the board.
In my heavily augmented d20 campaign I went a bit further and did the following (for anyone who might find these changes useful in their own game)-
Removed the concept of cross-class skills entirely (though for a while I considered keeping the class skill lists and the cross-class rank restriction but eliminate the 2:1 cost)
Increased skill points across the board (6+int is the minimum, with one or two classes having 10+int)
Consolidated some skills into a single skill but kept multiple ability dependency (Ex: Swim, Climb, and Jump into Athletics, but a Swim check keys off of Constitution, Climb off of Strength, and Jump off of Dexterity). Retaining these sort of sub-categories allows me to also keep feats and abilities that grant a +2 to Climb checks, but also add new ones that may give a +2 to Athletics.
Increased the minimum rank requirement for skill synergy bonuses to 10 ranks, as I've always felt that synergies should represent the ability to apply theories in the abstract to a different field - hence speaking to a greater depth of knowledge.
Borrowed a bit from Saga and implemented the idea of Core Skills, a small list of skills which are "core" to the character's concept and improve simply through use - these skills gain a free *rank* (not a bonus) every Even level.
Lastly I implemented Background Skills. The PC's, at creation, pick from the NPC classes and define a role, such as "Commoner (Farmhand)" or "Warrior (Watch Recruit)" and are able to put a small pool of points into a limited list of skills to reflect that.
These skill changes resulted in characters (especially 1st level) that feel far more fleshed out and "real".
Obviously that's a bit of a hefty change, and most DM's are largely going to tweak and twist the rules to fit their personal tastes. I think the overall skill system is one that, no matter which way you go, will be guaranteed to rub one group the wrong way -- as such the smartest thing to do would probably to present both systems as an option in the rules. I also think that in order to stay close to the stated goal of backwards compatibility, it would be a good idea to think hard on retaining the 3.5 skill points as the "main" option, and leave the more 4e/SAGA influenced skill system as a secondary option.
EDIT: Also, IMO, there's no reason why you can't have the more customizable (arguably) 3.5-esque skill system for PC's, and use the more streamlined (arguably) 4e/SAGA-esque skill system for easy/quick NPC generation. This is something I have always sort of done anyway, but mostly because I never felt the need to fully stat out an NPC that wasn't going to last more than a few rounds of combat (beyond HP, AC, Attack Bonus, DMG, Senses, and some notes on tactics). If they did, and survived long enough to become a recurring enemy -- that's when I would create/add more detail.