Gotta, be honest, the way Origins handles the gyms I've always thought was the best way to handle them because no matter the gym you get a battle appropriate for your level...well, unless you grind all your pokemon to level like, fifty but that's probably not going to happen. 

But that also is a thing with the 'set gym leaders'. (I think its also easier to abuse that way.) If it's a set thing, then someone can just grind their pokemon to level fifty and just completely crush a gym without any skill whatsoever.

But eh, whatever you think is best, mighty GM xD

to be honest though, the not being able to use all six of your pokemon for a thing is kind of a major turn off...but eh. I'll deal.