Well I still think Gyms should be type based... All of Ash's leagues (Barring the delightful Orange Islands and their 4 minigyms or rather tasks such as ice rafting or racing or target practices) have been type gyms. Why would that change? It is ANIME style battling!
Better idea, give the starting gym 12 points to do with whatever they please. If they want to get 5 basic pokemon, go for it, but they have to be of the certain type, OR evolve into it. But make it so that the pokemon that reside with the gym stay with the gym. If any of the leader's Pokemon are of that certain type, then they can use it in gym battles, but it stays with them.
I'm going to use Misty as an example because we've seen it so often.
The Cerulean Gym has a variety of different Pokemon. Goldeen, Shellder, Seaking, Luvdisc ect.
Misty has her own personal Pokemon - Staryu, Starmie ect.
Now, when she went travelling, she caught a Corsola. She uses that Corsola in Gym Battles as shown in the anime. BUT She keeps the Corsola with her.
Now, Dewgong, it stayed with the gym, and Misty has ordered it around in the gym in battle. BUT it stays with the gym as a gym Pokemon.
I think that when you leave the gym, you'll get to take 1 or two Pokemon from that gym with you.
Not to mention, when it opens... with those hypothetical 12 points I'll give an example.
I'm opening a Rock Gym, I'll catch a Geodude for 2 points, and a Onix for 2 points, and a Kabuto for 2 points and then spend 3 points evolving it. So then the gym has spent 9 out of 12 of its points. But only for the opening of the gym, allow Exp free evolutions for Gym Pokemon only.