Isn't that just a character flaw? I mean, if the character is only good on 1 type of stage, it shouldn't be the ruleset's problem to allow him to play one of those stages no matter what. And bowser isn't bad on the other stages, he just isn't brokenly-strong on them. Its like fox on huge stages, should we spread those out because fox "needs" to counterpick them against bowser because hes useless if they are all banned? No, fox can play on the mediums and be fine, albeit not as powerful.
Bowser isn't only good on 1 type of stage, he is just more dominant on small stages. There is only a small sub-set of stages that Bowser is not that strong on as well. So no, it is not so much a character flaw.
Bowser as a character very easily demonstrates the flaws of the cp system. With the old ban scenario, or even with group banning the way FC did it, Bowser and his opponent could eliminate every stage that either had a significant advantage on. That's great! But why is it called a counterpick then? You get no advantages and stage select becomes just personal preference.
I guess I just have more against the name or idea of a counterpick system. If characters should be forced to play on stages they may not be as comfortable on, then you should not be allowed to ban every uncomfortable stage. If you are meant to be able to remove all stages your character is uncomfortable on, even if it's just matchup related, then change the name of the "counterpick" process.
As an extra example Joe, because I know you remember this. Back when Pokefloats/Mute/Brinstar/Cruise/KJ64 were legal, I remember how a lot of players complained about there being 2 moving stages, or 2 stages with hazards. I can't ban out all of my problem stages, say the ICs players. Was there anything inherently wrong with those stages all being on? No, not at all. A lot of people brought up the points, "well what we want to test in a competitive setting is not players vs stage, but a player vs player scenario, and those hazard/moving stages detract from a competitive environment." There is nothing wrong with that notion either. All it does is change the metagame of the same characters. Changing the stage list did buff and nerf characters.
So what this really comes down to, in a game far more balanced than Melee, with far more available playable stages than Melee, where do we draw the line and define what we want. If characters should be allowed to play in advantageous positions and their opponents uncomfortable situations, then not every stage with those requirements should be bannable in a tournament set. If those stages should all be allowed to be eliminated, then change the name of the process after you have lost a game, and have a set basically on a neutral playing field.