FE, that's a good point, except that I give all classes a minimum of (4 + Int bonus) skill points, so it's a little evened-out. The heart of Traveller (CT and onward) was skills, skills, skills, and it really bothers me that a "typical" jarhead (with approximately a 14 Int) gets four [full] skills.
I've also modified the cross-class system such that cross-class skills cost 1/rank (just like class skills) but they max out at the cross-class maximum. (10-level character can have 13 ranks in class skills and 6 ranks in cross-class skills; if there's an odd skill point left over it (and only 1) can be carried to the next level; each of these ranks costs 1 point per rank.) This is a change I brought from my last fantasy campaign.
Does this muck around with the BAB/skill progression? Yes, but to be totally honest, they're not completely balanced as the system stands anyhow. There are a number of classes that are flatly superior - or flatly inferior - to other classes.
Do I want to tweak them all so they're "perfect?" Yes, yes, I do. I'm a rules tinkering addict. Am I going to? No, my last <fantasy> campaign was a heavily HEAVILY modified d20 system, and my players didn't really care for it much. This campaign will be a lot closer to "book" d20, with only my very favorite house rules - like the cross-class skill cost and replacing the vehicular and starship combat systems with
Renegade Legion's system - will be applied.
Or so I state now....I have no confidence in my willpower to resist more changes later.