Agreed on the rogue point -- they're definitely underpowered. To be effective they need so many skills.. eg if you want to be a stalker, you need hide in shadows, move silently, a weapon skill, and either alchemy or magic to get cat eyes, (plus light armor, but you don't need to pump it for DR, I guess) so four central skills. I've found with other characters that two is ideal, and three is a lot. I didn't actually play through with a rogue, so maybe you only need hide/move up to 4 or 5 ranks, but still.
I liked the Exile/Avernum (sorry, those pop to mind, I know there are plenty of other games that do it) method of having different skills cost different amounts of points, but then you lose the elegant simplicity of the current Eschalon system. *shrugs* One possibility would be lumping skills, for example have move silently and hide in shadows be put into a single skill ("Stealth", maybe); perhaps throw skullduggery and lock picking together (can't think of a name off the top of my head

). Just an idea, sorry if this has been suggested before, or is off topic.
Edit: more ranting on rogues:
The idea of so many rogue skills (hide, move silently, spot, traps, lock pick, etc) comes directly out of D&D. The reason it works for D&D is that rogues get twice as many skill points! (8+INTmod vs. 4+INTmod for most, if you're into that sort of thing) That's not doable in Eschalon, because there aren't hard classes. To keep the simplicity, I do think joining skills together is the way to go.
cheers
~nepharis