It sounds like a good idea but with so many pet colours and so many new petpets coming out all the time, along with the fact that people can have wildly different taste when it comes to petpets...it could prove difficult =) When it comes to looking for matches for most things the petpet puddle is quite handy anyway in it's groupings but I really wish it would show ALL petpets rather than just those that can be painted. There isn't anywhere on neopets itself that actually lists all the petpets which can be frustrating.
When NC is up it's quite handy to search for matches on the Petpet board as all requests have their own title so by searching for "maraquan and acara" for example you're guaranteed a few threads with a few choices
Good luck if you decide to go for it though, it would be quite hard to layout but if completed I'd be an avid user!