I personally don't see Final Smashes to be entirely game breaking, telling you the truth. You see, in order to actually use a Final Smash, the Smash Ball, first off, needs to spawn. Once it does, you'll have to divert attention away from beating your opponent to hit a hard to reach ball that may set you up for an early death due to your position. Also remember that the Smash Ball can be beaten out of you when you get it. If an opponent if good enough, he'll just render the Final Smash chase meaningless as he combos you straight to hell.
On top of that that, even if you do get the Smash Ball powerup, you need to take into account of two major factors: Positioning and timing. Imagine, if you will, that you are playing on the Castle Siege level. Due to the constant changes to the level, using something like Peach's FS or Fox's Tank becomes a liability since you're either going to lose out on those important healing items or, due to your size, you'll die a quick death due to lack of mobility. While I know every stage is different, there are plenty of tactical positions that can leave certain FSs useless. This alone would make the execution and success of FS more rewarding since you are overcoming the shortcomings of said FS and connecting in situations that would normally be difficult.
For those who believe Final Smashes are broken themselves, not true. Super Sonic is way too loose for his own good. He can literally kill himself trying to kill an opponent. Samus requires the player to remain stationary for a slow blast that can be dodged. Pit's Goddess army is easy to dodge from the videos I saw, with only one actually hitting the opponent. Metaknight's FS is really just Raging Demon, requiring the attack to be close and still to the opponent. I can go on but this will do just fine. I personally see this no more broken than other fighting game Supers, which are really meant to reward the user to finish a match quickly despite the opening he is subjected to due to the utilization of the attack.
Anyways, this is my two cents on the issue and I think it's not bad for a first post. It's definitely up to the community as a whole but I see no harm in allowing FSs in tournament play, personally.