I think you need to start by describing the goals you're trying to achieve by changing the system. You say you're very dissatisfied, but you don't really describe what's dissatisfying. You also say you want something more comprehensive, but I'm not sure what you think is lacking. Then you mention 3.0 skill system but, to be honest, I find that system equally comprehensive and needlessly more complex (and 3.5 is worse with all the situational modifiers). You think there should be more skills? You don't like the proficiency system? You think a 10th level character should expect to automatically succeed on skill rolls?
My problem with skill systems in general is that there are only two broad types of systems. The first one has fairly generic all-encompassing skills that you get to pick a few of. That's not terribly realistic because characters can do things that don't seem related and some skills just become must-haves. However, the alternative systems that say, "Our Zombo.com system has unlimited skills! Anything can be a skill!" can be much worse. The problem with those systems is that you still only get a limited selection of skills, and because the number of skills is so diverse you stand a much better chance of not being able to even roll a die because the DM thinks that, for example, modifying the starship navicomputer requires Electronics instead of Computers, Astrogation, or Repair. It's a pigeonholing problem. Skills stop being about things you're good at and instead define everything you can't even try to do.
So, that's kind of what I mean. What kind of outcomes in game play do you want for a skill system? What do you intend for it to accomplish in the game itself? Define your problems, describe your desired outcomes. Be specific. "I want more skills," isn't an outcome but, "I want the players to have to make tougher choices," is. "I want bigger bonuses," isn't an outcome, but, "I want skills to represent a broader range of expertise than 'skilled' and 'not skilled'," is.