Okay, so with the advent of Atheno's new gym I have a bit more to say on the topic of gym brokenness. Basically, both sides are B8P3, the arena has some (but not overpowering) Water advantages, and the opponent's team must share one common type. While I don't exactly agree with the one common type thing (perhaps B5P3 with two shared types allowed?), this is a step in the right direction.
I think the base disagreement here is how hard, exactly, we want gyms to be. Do we want any very good player with a strong, built-up team with a few mons effective against the gym type to be able to beat that gym? Or do we basically want only gym leaders super-effective against the gym's type, playing at the top of their game, to be able to win? Right now, the gym system is strongly tending towards the second option. Basically, the challenger has no advantages short of being able to bring whatever three Pokemon they want. But I'd argue that this may hardly matter anyway, as with the ridiculous assortment of secondary types and Abilities available to the majority of types in Pokemon, quite often the CHALLENGER can get counterteamed...not the other way around. Then there's the whole issue of the arenas, which just further the issue.
tl;dr: How hard do we want the gyms to be?
Ten million fireflies