Here's Gym idea 12346789 (yes no pesky 5!)
What if everytime you entered a Gym it gave you a Random, order.
You'd have a different potential encounter everytime you entered a gym. Blissey could be 1st, 4th, or 10th.
When a Gym loses Prestige whichever pokemon was "First" in that random order is dropped out.
You would also have to resmooth the 50000k curve. 5k each. No more 2 free spots on conquering either. a Level 1 Gym would need 3k to prestige up, same as a level 9 gym. Since order would be random, the effort to get into gym should be same.
Answers
Terrible suggestion, there will be no point in powering up pokemon and Leveling up trainer account
with your suggestion its possible for a trainer Level 5 put 10cp Pigey and be the last out.
What are you thinking?
5000k each prestige is an OK idea. But you can never get more than one pokemon in a busy gym.