No matter the system, this is something you will always run into in my experience. And no matter the system, your training with it will be more important than the system you decide to use. You mights start our with “00 = Atlantis: The lost Empire & animal = Mole” but you have to get to “00 = Mole”. When you reach that, the system you used to get these is no longer of importance.
One major strength I found in these types of systems (my 2-digit PAO started very similar) was that it becomes easier to actually pick the characters you love. The structure is also clear to imagine beforehand what kind of characters you will end up with.
A weakness I found mainly when adopting this system for my millennium system is that not all categories allow for ten good characters. I often thought I had a good category only to find 8 or 9 persons there.
while difficult indeed, I think that any sort of limitation on a 3-digit system will make it difficult. I myself found it easier to find 1.000 persons with categories (without the trait limiter) than I would have with the major or dominic system.
This is pretty much how Flauwy back in the day (Link) and myself (Link) created a millennium system.
The attributes might prove to be less of a rule and more of a guideline in the larger systems. I took it a bit less strict myself and worked with number associations rather than traits. 282 is Sokka from The last airbender, because 200 is cartoons, 80 is the last airbender (8 looks like aang on the air orb), and 2 looks like a flying boomerang, so Sokka.
Be sure to try this a lot. Some token actions do not work well with other characters. An example I struggled with was flying for example, seeing the Hulk flying was memorable, but seeing Angel flying was not.