[video=youtube;M1NebBaQ8ow]http://www.youtube.com/watch?v=M1NebBaQ8ow[/video]
The video above displays every Final Smash in the game. It's plain to see that some are more powerful than others. After all, it's difficult for HAL Labs and Nintendo to make the Final Smashes balanced in power just as it's difficult to balance all the characters in the game. I am a general supporter of Smash Balls and items in general; I find them to be a fun novelty when they're turned on, but I am also a serious enough player to know when to turn them off and have a battle uninfluenced variables like items. Also, getting to the Smash Ball and keeping others away is an accomplishment in itself and should be rewarded, although there is blatant unevenness in this method on large maps such as Hyrule Temple and New Pork City.
Two of the most obvious divides in the potency of Final Smashes are the automatic vs. manual attacks and OHKO vs. Percent Damage. Manual attacks are usually pretty powerful, as long as control is easy and attacks are powerful. For example, Sonic and Snake's Final Smashes. Instantaneous Final Smashes are usually OHKO's and deal high Percent Damage, but are limited in the number of opponents they're able to effect. With so many different kinds of Smashes, it's only natural for people to compare them and rank them like they do characters on the Tier List.
The thing is, they're hard to compare. You could make all the Final Smashes manual control or OHKO or whatever and place them all in the same category so they work similarly, but that also makes Final Smashes dull. Competitive players can just turn off Final Smashes, and new players will be drawn into the game by the variety of Smashes. Truthfully, I like the system the way it is.