A different approach you might be willing to explore is how 4E does skills, where you pick skills to be trained or untrained in. But where 4E did some serious generalization, go the opposite direction and super-specialize them. Bring back Innuendo and Intuit Direction as separate from Sense Motive and Survival; re-split Forgery and Decipher Script and Linguistics; make Sleight of hand separate from Pick Pockets; divide Spot, Listen, and Search; bring back Jump, Tumble, and all the other skills that used to be their own thing.
But with the increased number of skills you need to have a proportionately greater number of "training points" (or whatever you want to call them). Because instead of computing individualized skill ranks for each skill (which would only be fun for CPAs), characters might choose a certain number of skills to be "primary skills", some to be "secondary", some to be "hobbies", and would treat the rest as untrained (whether usable untrained or not). Each category of aptitude would represents a certain level of expertise (not just an all-or-nothing approach as 4E does).
"Primary skills" would have the maximum bonus appropriate for your character level. These are your specialties.
"Secondary skills" wouldn't carry as a big a bonus as your primary skills, but you should be able to do a decent job with one in a pinch if you roll well.
"Hobby skills" are the equivalent of "rank dipping"--equivalent to taking a single rank, though even this low bonus might advance every 5 levels or whatever.
As in 4E, each level of training has a fixed bonus granted per character level, which advances every so often. While this loses some granularity in the system in one area (individualized skill check bonuses), you improve the granularity in another (being better at auditory perception than visual, or being a better pickpocket than a juggler).
Any given class would have X number of each category they could select at character generation, which will be roughly analogous to the number of skill ranks they get now. Suppose the new list of skills consists of 50 skills in roughly the same proportions of Strength, Dexterity, Intelligence, etc. that they have now, and there is roughly the same percentage of "rogue-y" skills of the total list as there is now. Rogue would have to have at a minimum enough primary, secondary, and hobby points (or whatever you want to call them) to give the class at any given level more or less the same level of skills capability that it had before--slightly more slots than Rangers have, and both will have significantly more slots to use than Fighters.
Unlike RAW, there is the potential for differentiating between classes that get the same number of base ranks per level--two classes might have gotten 6 ranks/level in the old system, but one class might have a larger proportion of secondary skills vs. primary skills than the other, because that class likes to be more versatile than the other. The "dabbler" may have a higher total number of trained skills than the "specialist", but they will be roughly equal in terms of capabilities with skills.
The game mechanic that grants a skill check bonus for a trained class skill would still be there, but whether it should stay at +3 or not, I couldn't say, not without hashing out more of the specifics behind these rules changes.
There should probably be an option for trading out a primary-skill slot for two secondary-skill slots (or 1 secondary and 1 hobby, etc.) but this would have to be well-designed to prevent exploits. Perhaps a feat for buying additional "hobby skill" slots, or a feat for upgrading a secondary to a primary.
