I know very little PHP, and that's about it.
I'm going to learn a heck of a lot in the summer is what I'm planning on doing.
My Suggestion:
I had to think about this for a while, but I think I have one, well more like a billion.
1st Suggestion: I'm going off of the whole "fly" idea but; Trainers who have beaten all 8 Kanto Gyms have the ability to /fly [CityName].
2nd Suggestion: We could have "statues" of trainers that show up in a city/route/cave/place. They would have a slim chance of spawning, and then they would attack you. They could have like the same amount of health (10 bars) as we have & the farther into the game they are, the more weapons/armor they get. (That's a bit out there, I don't expect a "yes" to it really)
That's about it for now... But I'm sure I'll do more stuff.