I'm 90% of the way through implementing this. It'll be my first NVSE-required mod, though I'm sure I'll release an NVSE-free version with less functionality.
To be released as part of the XFO package at XFO-NV.com
As it stands, it's easy enough to remove the skill cap (XFO-NV itself does it, so does my pacing changes, level/skill cap remover at http://newvegasnexus.com/downloads/file.php?id=39055) -- but at this point, all that does is let you keep leveling after all your skills reach 100. The game "knows" what the real (>100) value of your skills are, but stops calculating everything past 100.
I'm adding some changes that take effect every 10 ranks in each skill after SL100. Here's what I've done so far
Barter: every 10 points reduce buy price by 5%
Energy Weapons: Every 10 points increases armor piercing:decreases enemy DT by 2 (would 1 be more balanced?); increases VATS acc by 5%
Explosives: Every 10 points increases explosion radius by 5%, increases your DT vs. explosives by 2 (would 1 be more balanced?)
Guns: Each 10 points increases crit chance by 1%, increases VATS acc by 5%
*** Lockpick: ??? (NEED IDEAS!)
Medicine: Each 10 points, Stimpaks get more effective (20%; can't do less; might change to 20% every 20 points), drugs last 10% longer
Melee: Each 10 points, increases damage 10%
Repair: Each 10 points reduces gun/armor wear rate by 5%, increases repair effectiveness
*** Science: Each 10 points reduces energy ammo usage, (need second effect)
Sneak: Each 10 points increases "chameleon" effect by 5% while sneaking
*** Speech: (NEED IDEAS)
Survival: Slows hunger/fatigue/thirst rates, increases non-combat regen
Unarmed: Each 10 points increases UA Speed by 5%, reduces UA AP usage slightly (2%?)
ANY ideas, feedback, thoughts, etc, are hugely welcome. This is probably 80% done, though I'm working on an easy way to display the "real" skill amount (pipboy and skill upgrade page still only show up to 100 -- if any modders know how to change this, please let me know! -- but I can put in a hotkeyed messagebox to show all the values, and the console will also show those values.
I also need ideas for Science, Speech, and Lockpicks.
Next step, I'll add some epic perks for levels >30 and skills >100!