I recently ran a small tournament with a few friends (it was only about 18 people or so), and found that this seems to work for stage picking:
First Game Starting stages were FD, Battlefield, Yoshi's Island (Brawl)
Second/Third Game stages were FD/Omega, Battlefield, Yoshi's Island (Brawl), Prism Tower, Arena Ferox
We considered other stages, but we basically did the natural thing all tournament. Each game, both players ban a stage and the loser picks which to go to. In the first game, both players ban a stage and go to the remaining stage.
IDK, we wanted to play it safe instead of push to "make" more stages plausible. Personally, I find that it works best. There may be a few other stages that are good, but honestly we're even being a bit pushy about some of these stages.
For instance, Yoshi's has bad ledges, and the shy guys are a pain when they swoop in while you're approaching. One time I was going against a Fox player, and at least 6 of them swarmed him while he was doing his FAir. It was nasty.
Prism Tower would be a really good stage, but the main platform shrinks during it. It makes it unreliable, and almost scary to stand on for more than a few seconds. It gives a mindset of being more Aerial than ground-based. Which isn't good. However, the stage itself is good in an overall standpoint, it's probably more of a personal thing that I don't like the main platform shrinking.
Arena Ferox is basically Pokemon Stadium from Melee. Just a good bit less...odd. I like it, and I think it fits, however, there are a few destructible parts to it, that can be a bit distracting, but I've never run into the issue.
In my honest opinion, we shouldn't force or "make" stages good. We should accept them for what they are, and then decide if they are balanced.