I think it's largely an excersise in futility.
The only way you can see how these balance out is by playtesting them -- the same way you can see how CR's and ECL's are done. You can't point-buy/min-max it. It's all about perceptions and eyeballing.
To take those extra skill points at first level as a rogue, what are you giving up? At first, just a few cantrips and magic missle, really. But eventually, 9th level magic...are a few extra skill points worth not being able to cast wish?
It depends upon the campaign, the character concept, exactly how important to you having a lot of skills is, etc.
It's an eyeball. It just so happens that the core classes are the best-balanced things I've seen in D&D since...well...never.

Heck, even compared to the few other systems I've tried. Just because, if you want skill points, a rogue is better to take at first level than any other class, doesn't mean that it's unbalanced.
After all, think of what the "time before 1st level" represents -- training. Training as a rogue emphasises skills. Training as a Sorcerer emphasises wieldin' magic and cleanin' out your familiar's cage.
So....yeah....not so much imbalance. I don't see everyone takin' Rogue at first level, so I don't think it's a problem so much, ya?
