I think option nr 3 is the best solution in my opinion. while it would require more time to develop it would be a chance to improve this already great fangame.
so about your questions
1. You can call the gym assistant (in my case it's the old gym guy) and he will tell you the reputation, after you gain enough reputation your rank will increase giving you acces to some areas and features.
2. They provides revenue so income from what I understand so far...
you use pokegear to call the gym leader hotline, choose vacation information and take a vacation then you go talk to the receptionist
I have a question about misdreavus-how do I evolve it to breezian mismagius? I tried dusk and fire stone but they don't work