They were underrated as hell by critics and fans at the time but I'm incredibly fond of them. A bit flawed, but they were fun. The games were also moving in a direction that would have reintroduced wild Pokemon to Orre too, so it's a damn shame we never got a third.
They could have taken it in a very interesting direction with Pokemon stealing still being pandemic to the region, but with enough wild Pokemon out and about so as to be like a main game. Keeping that E10-style Pokemon vibe alive. Say you pick a standard starter Pokemon and shortly after the campaign begins and you've bonded a little bit with it, YOU are the one that has their Pokemon stolen. From there you're taken under the wing of a man who may or may not be one of the previous protagonists, and are given an Eevee with the ability to sniff out the 'corrupted auras of dark Pokemon' (read between the lines, it's psychedelic drugging and other nasty things). From there your personal mission becomes to rescue your Pokemon, crush Team Snaggem or whatever it's spiritual successor is called, and rescue these stolen Pokemon.
The game could give you a lot of morally ambiguous situations and options to really make the story your own. Do you track down the original owners of the Pokemon you save, or do you keep them for yourself like your mentor encourages you to do? Do you let the person who took your Pokemon die when he/she pulls some stereotypical 'I lost, time to jump off something really tall like a badass to my death' scenario, or do you save them? I dunno, just random scenarios that keep with the original edge-lite vibe of Colosseum and to a lesser extent XD that makes it feel more like a different character than our usual Pokemon protagonists, much like Colosseum originally did.