If the house rule's gamed, there's a chance of a minor imbalance
The special ability uncanny dodge scaled differently in Dungeons and Dragons, Third Edition, where it was tied to, of all things, what's now the special ability trap sense. Advancing uncanny dodge meant looking at the rogue's level advancement, computing a character's effective rogue level based on how many levels the character had in classes the grant the special ability uncanny dodge, and, from that, first gaining improved uncanny dodge then an increasingly higher bonus to trap sense. Yay?
But Dungeons and Dragons 3.5 changed this, granting the special ability improved uncanny dodge when uncanny dodge was gained a second time, yet providing no mechanism for advancing improved uncanny dodge, therefore leaving bereft a PC who receives three or more iterations. Boo. Hiss.
I mention this because that makes reasonable your instinct to want to give the character something despite the game saying the character gets nothing, the system at one point having supported (albeit poorly) your instinct. My guess is the decision to streamline uncanny dodge—like a handful of other Third Edition to 3.5 changes—was made hastily and insufficiently considered, and I respect wanting to correct that error.
Anyway, nobody likes leveling up an getting nothing. The proposed house rule seems like a good one, even if it's ruthlessly exploited. Just in case the full ramifications haven't been considered, below's an example of a possible ruthless exploitation.
| Character Class Uncanny |
| Level Level Dodge |
| 1st Rogue 1 N |
| 2nd Barbarian 1 N |
| 3rd Rogue 2 Y |
| 4th Barbarian 2 Y |
| 5th Survivor 1 Y | Savage Species 89-90
| 6th Warblade 1 N | Tome of Battle 20-6
| 7th Whisperknife 1 Y | Races of the Wild 135-9
| 8th Yakuza 1 Y | Oriental Adventures 55-6
| 9th Warblade 2 Y |
It's a lot of work for this, and it's still not awesome. Such a character must be a halfling and probably must take two flaws to meet the requirements of his prestige classes but, at level 9, has a competitive base attack bonus of +6 and weird but playable base saving throws of Fort +8, Ref +9, and Will +2. (Don't judge—a Rog9 only has a base Will save of +3.)
And, if the above character enters play as a constructed character rather than advancing through these levels organically, his backstory will be amazing.
That said, under the house rules described, this character's player'll have his choice of four rogue special abilities for his character before his character's level 10. That's a lot. Were this house rule present in a campaign in which I was participating (and were the party a reasonable collection of not-totally-optimized PCs), I would carefully consider playing a character like this.1
However, if the players can be trusted not to game the house rule, that's cool. I mean, really, the house rule isn't so good that it automatically makes classes granting uncanny dodge tier 1 or anything, and probably won't even really affect the balance of a character with such a bizarre combination of classes vis-à-vis a straight-up highly optimized flask-throwing, Sleight of Hand-exploiting rogue. The proposed house rule may make folks think hard, though, and if that's a good thing depends upon the table.
Instead of either getting nothing or getting a rogue special ability when a character would gain his third iteration of uncanny dodge, have the player pick a feat for his character to gain from a list of feats the DM and players develop. This alternative simply avoids the question of whether rogue special abilities, if granted early or by a class other than rogue, are unbalanced.2
1 That's mainly because Lady Luck hates me, so whenever I play a character that can gain a special ability that eliminates the need for me to roll dice, I take it. Having the special ability skill mastery available that early in my character's career would be so awesome for me, I might take the special ability skill mastery twice and never roll a skill check again. (Honestly, I think most players would first take the special ability crippling strike or opportunist.)
2 The old school DM in me (a la the year 2000) thinks that increasing the character's trap sense by +1 upon each the third-or-later uncanny dodge iteration might be an acceptable alternative to nothing, but that also sounds sort of insulting, given that the special ability trap sense is widely considered to suck. (Forced into such a situation, I'd try to get Wis 13 so I could take the feat Dungeoneer’s Intuition (City of Splendors: Waterdeep 144); then it's almost something.)