I don't remember the perks (at the quarter points) doing anything really significant since you reached them inevitably if they were on the progressive path of your character, and not by choosing whether or not to invest in them.
The quarter points (25, 50, 75, 100) is where major changes would occur. Repair for instance you would be able to use the hammer much more at each quarter point before it broke, until at 100 you never had it break and would only need one the rest of the game. The spells were the same way, you had to be atleast at 25, 50, 75, 100 befpre you could even use them. Each point was significant.
I wouldn't necessarily suggest that exact solution though, because there were inherent flaws in that you could manipulate the system (running or sneaking) for no reason to boost levels or just casting spells for no reason to boost levels.
There is something simliar in Vegas already, but not exactly. The perks act the same way, where if you have like 70 Repair Skill you can get the Jury Rig perk. So it was similiar in that regard.
If anything the guns need to be split into more categories for skill pts... one handed, two handed, sniper, etc. Switching to another gun regardless of type gives you the same ability? That doesn't make sense, just like Unarmed and Melee are different because each or unique types of attacks and need separate skills. Of course at this point we're adding quite a bit of complexity...