So, the two aims of this alteration - make thief skills better at low levels and marginally more difficult at high levels, and provide a means of significant differentiation between thieves by way of skill choice.
The essential conceit here is to make thief skills function like tiered proficiencies, with target values 22+/18+/14+/10+/6+/2+. Find Traps and Hear Noises both have base difficulties of 18+ (the value at which anyone may attempt them), while Open Locks, Remove Traps, Pick Pockets, Move Silently, and Hide in Shadows have base difficulties of 22+ (not possible to use untrained). Backstab has a base value of +2 to hit and x1 damage, then progresses +4x2/+4x3/+4x4/+4x5. Climb Walls, Read Languages, and Use Scrolls are all odd. I'm inclined to use Arcane Dabbling as a precedent for Use Scrolls, with a base DC 22+, base trained DC of 18+, and then make advancement 'easy' since it usually grows at 2/level, unlike most of the other thief skills - perhaps 18+/13+/8+/3+ rather than the usual progression. Climb Walls and Read Languages both fall into the 'start off easy and don't grow that quickly, but not available to non-thieves' category. I guess --/6+/2+ would work for both; sort of considering adding another tier, for --/10+/6+/2+, but curious to hear some feedback first.
A class whose thief value provides it n skills (after any tradeoffs for proficiencies and custom powers) starts with n skills 'trained' and the remainder untrained. For example, assassin's thief value of 1 provides it 3 skills. It starts with Hide in Shadows, Move Silently, and Backstab trained, at 18+, 18+, and +4/x2. It can also Find Traps and Hear Noises on 18+ (their untrained values), but cannot Remove Traps (for example) because the untrained value of RemTraps is 22+. A thief, by comparison, gets 10 skills, and chooses Read Languages as the one to not be trained in at 1st level. This gives a 1st-level thief 18+ for most standard thief skills, 14+ for Find Traps and Hear Noises, 6+ for Climb Walls, 18+ for Use Scrolls, and +4/x2 backstab. If you wanted to keep the 'core skills' closer to the normal values, choose Find Traps as the untrained; then you have 18+ on Find Traps like a normal 1st-level thief, but gain Read Languages at 6+ (this is one reason I think a 10+ tier for Climb and Read might not be a bad thing).
The number of 'skill advances' a class receives per level is a function of how many skills it has. A class with n skills should receive n/4 advances per level on average (I considered taking the Level-Lock Tradeoff rules and basing advancement off of those, but those were going to be more complicated, and would've done poorly with classes that did partial trade-offs like Venturer). Thus, an assassin with three skills gains three skill advances spaced out evenly over every four levels - one each at 2nd, 3rd, 4th, 6th, 7th, 8th, 10th, 11th, 12th, and 14th ought to do. A thief with 10 skills would get 2.5 advances per level, so 2 advances at each even level and 3 at each odd level after 1st. A character may spend an advance to raise the rank of an existing skill by 1 (eg, Hear Noises from 14+ to 10+) or to raise an untrained skill to trained (so an assassin might slow his stealth growth to pick up Climb Walls at 6+ rather than burning a class proficiency on Climbing).
- Super-stacking everything into one skill. A third-level thief could max out a single skill at the expense of all others if he so desired. At the very least, a restriction that one can't put more than one advance per level into any given skill might be wise.
- Backstab - 3rd-level assassins with x4 backstab are a concerning possibility. Backstab might warrant a 'no more than one advance per three levels' exception. I think I'm OK with people accelerating their backstab progression some at the cost of their skills, but not all the way up to once per level, or even once per two levels.
- Interoperability with existing +skill proficiencies. I think this would mostly work itself out; Skulking still gets you +2 to Hide in Shadows and Move Silently, Lockpicking still gets you +2 to open locks, and so forth. I'm inclined to keep 2+ as a hard floor for difficulty, though. Where this does get weird is with proficiencies like Climbing and Eavesdropping that let you do X as a thief of your level. Again, I think we could mostly leave those alone and have them refer to the original skill table. About the weirdest I could see coming of this would be like... an Assassin with Alertness and Eavesdropping who also put advances into Hear Noises. But that would be rather silly because of opportunity cost, both in class proficiencies and skill advances.
- Hijinks. Fortunately, the hijink income results are a function of level, not of skill result. Being specialized in a single skill would let you succeed more often, but would not boost the yield per successful hijink (except Smuggling and Stealing...). I'd also argue (from the heist genre, at least) that thieves should be specialists in a relatively narrow range of hijinks. One change I might be concerned about here is that Find Traps got easier, which makes Treasure Hunting more appealing. On the other hand, I'm a firm believer that Treasure Hunting is a vital component of thief party-support play in the mid-levels, so... not horribly concerned about making it slightly better. In any case, it might be prudent to slightly adjust hijink yields down across the board to account for the possibility of increased success rate at low/mid levels. On the other hand, keeping the high end the same is also somewhat appealing, since that's how realms are funded... I'd also not be averse to building a streamlined 'abstract/generic hijinks' system, which largely dispenses with the link between individual skills and risk/reward balance. Instead, choose a risk/reward level, and make a throw with a target value based on your level. More like the Magic Research throw than being linked to individual skills. And then hey, we could add Dex in there like Magic Research adds Int.
- NPCs. I don't want to have to choose a bunch of skill advances for NPC thieves. Fortunately, this should work sort of close-enough to the book thief skill values over time that I shouldn't need to for mooks, but if there were an infamous cat burglar repeatedly burglarizing the PC lords' vaults, I'd be able to customize for that.
- More generally, complexity. Choosing 2-3 things per level as a thief is a lot slower than just rolling HP and maybe choosing a proficiency like most classes do. The only classes that gets something comparable in complexity are arcane casters, but there it's somewhat delayed because spell formula availability for repertoire loading is limited. On the other hand, this is a lot simpler than a full skill-point system, where a thief would get like... 10 points per level to allocate between skills. I could see trading two skills for proficiencies on the thief, and then making is a flat 2 advances per level for simplicity's sake, with the dropped skills being Use Scrolls and Find Traps, and the gained proficiencies being... I dunno, Arcane Dabbling and something else useful. Why the heck isn't Disguise on the Thief class profs list, anyway?
- Levelling rate. Nominally this should keep the power of the class close to its original value, but that's a hard thing to tell without any playtesting. Being able to pick and choose capabilities to specialize in might be worth an XP surcharge.