Okay, just a couple of challenge ideas that popped into my head ^^
1: 'Mono nature' challenge
-Here's how this one will work; you have to complete any pkmn game using pokemon of one nature only. The person who comment's under you choses that nature, based on what they think of your personality (profile, signature, comments etc). Also, just to make it slightly more fun, you can only catch pokemon that slightly resemble that nature; ie if you get 'rash' you could have a primape or weaville, but not a alakazam or slaking.
2: The currently unamed challenge (gym swap or something?)
-This one's gonna be difficult to explain, so sorry if you can't tell what I'm saying. Each time you defeat a gym, you have to change you pokemon to ones you catch after it. Example: On Firered, you have your starter and a butterfree when you defeat Brock. You need to go to the next route out of Pewter, catch some pokemon, deposit the butterfree and starter, and use those. The rules would be no legendaries, no cheating (it's really not needed) you can't go out of a city with a gym leader to a city you haven't been to yet; ie you can't leave Cerulean and go to Vermillion until you bet Misty; and you can't catch pokemon in previous routes once you've bet the gym leader.
Why can't I do them: First one needs work, I can't explain the second one without a huge lecture; time constraints, I probably wouldn't finish; and I don't think I'd be the best person for looking after a thread.
Enjoy!