Hmm... what I did with monsters that offered LA was that I made up an "LA" class that had a d4 HD, 2 skill points per level, no class features, and a bad BAB and saves (all of them) progression, and anyone taking a race or gaining a template that had LA of X gained X of the "LA" class. I actually wasn't sure whether or not it was a good idea. I don't know why I did it. Oh well, nothing horrible came of it, so it's all good, haha
Curious. So, this would either help saves or leave them alone, depending on the LA. As for HP:

A goliath barbarian 1 (ECL 2) would have 4 + d12 (averages to 6.5) + 2*con modifier hp, rather than 12 + con. They'd have a more random HP total, and tend to be ahead if their con modifier was 2 or higher (which it probably would be at anything from 25 points buy up), and behind it if was less.

A half-dragon barbarian 1 (ECL 4) would have 4 + 2d4 + d12 + 4*con modifier (which averages at 15.5 + 4 * con) hp, rather than 12 + con modifier, and would therefore be significantly less fragile - no bad thing, on the whole.

And as for skill points:

A tiefling rogue 1 (ECL 2) would have 4*(2 + int) + (8+int) skill points, rather than 4*(8+int). So the point of equilibrium would be if 5int +16 = 4int+32, ie if you had an int mod of +16; all in all, the tiefling would really be hurt by this. Obviously this would matter a lot less if you had 4 skill points per level, and be an actual positive if you had 2 skillpoints. At higher LAs... well, you wouldn't be playing a skill monkey anyway. Which skills would be class skills?