Something tells me that they won't be used in tournaments. Maybe a few at the beginning, but I'm skeptical.
1. Some Final Smashes are a lot cheaper than others. Of course, it's not as if any one is so broken it simply can't be avoided. But then we haven't even seen all of the FSes in the game. We haven't even explored potential move-FS combos.
2. Despite what some people say, it's technically not part of the character's moveset since it requires an item, so that doesn't justify the inclusion of the FS.
3. It's an item.
4. Somehow I don't think people would appreciate the dynamics of the appearance of the Smash Ball. Both players would likely drop their current strategies and go for it, so as to prevent the other from doing so. And then, since the Smash Ball can be hit out of you and eventually disappears (I'm not 100% on the last part; I could've sworn I read it somewhere), there's the immense provocation to just use the thing ASAP.
5. People whose characters' FSes aren't quite up to snuff (ex. Samus' if ZSS happens to be a sub-par character, Pikachu's, Wario's, etc.) would complain a lot, and a lot of people might just think "Screw it!" as a result.