It's all a matter of character ability I guess. It's natural that Radec can get like fifty billion kills with his because he can utterly rip you apart with his bullet storm, but Spike's best weapon is that satellite laser. It'd be stupid for him to get more than three max since he only gets one shot. Kratos get super huge, sure, but he's restricted to himself, so of course he needs ranged abilites to maximize efficiency. I don't understand Sly's special at all, but I guess that's apart of one of his games, and so on and so forth for everyone else.
I get your point. About Spike, though, his S3 could of been catching monkeys (everyone turns into monkeys, like mummy with Drake). So I think it has to do something about variety... Maybe reduce time of effect of some S3's? Ah well, that ain't happening and I'll just get used to this.
I guess that make sense if something in Ape Escape actually turned people into monkies. I've never owned the game, so I wouldn't know if that happens or not, but that sarcophagus in Nate's level three really does turn people into zombies, plus, he's human and has no super amazing weapons like Spike, and has no outstanding abilities, so they had to give him something effective, and that makes a lot of sense. The only thing not accurate about that special is that it took more than one shot to take them out. Those zombies were powerful. Only a shotgun actually eradicates them with a single shot, and even then, that was dangerous because one hit from them would seriously injure you.
I'm bored so I made a list...
wipe screen 4
fat princess? unique?
For your list, I think "upgrade" can be divided into Godmode and Vulnerable Opponents (i.e. Raiden's basically just helplessly puts his opponents in boxes while a super like ST or Kratos still has their opponents able to dodge)
"The Dirty Casual"
I think it was SuperBot's idea of variety (as someone above mentioned) and individuality. If every Level 3 Super was a screen-clearer, well that wouldn't be very exciting, now would it? But as a result, some Supers are superior than others which is the difference in balance.
But at the end of the day, every Super has its advantages and disadvantages.