One reason I like conservative stage lists is because it's likely to prevent whining/johning.
Like in 1337's aforementioned scenario, player 1 would be like 'WTF, I wouldn't have lost to this guy if we played on less hazardous stages.' And then arguing ensues, and probably a lot of stupid **** gets thrown around. Unless the vast majority of people at the tournament agree upon the stages, I wouldn't bother.
Perhaps one idea would be not to have a set list of counterpicks, but hold votes with all the players before asking them whether they'd want some of the more controversial stages legalized, like Port Town, Yoshi's Island (Melee), and others. Whichever side gets more votes for each stage determines whether it's legal in the tournament or not. Since every tourney is going to have a different cast of people, it makes sense to cater the event towards the people who actually showed up. The hope of being able to go and affect the tournament would probably increase attendance at the events, since some people would look at a liberal stage list and go nowhere near the tourney.
So yeah, Direct Democracy for the win with determining controversial counterpicks. Legalizing it based on the people present would probably be the best idea, instead of pre-determining it beforehand. This way in case a change is made, it won't be as uproarious. Since some may be like 'What the hell, this stage was/wasn't legal when I signed up!' kind of thing. Leaving it up to the people present is the best choice in my opinion.
But I've never been to a 'real' tournament so I don't know how it'd pan out. I mean, I can't imagine it being too difficult to hold a vote with such a small group of people.