Yeah you may have missed my point. I realise that the traits are beneficial when used correctly and you can waste them, however, there's relatively no thought to using a lot of the traits, it's generally just a case of press trait and the character becomes better with no consequence and so there's no thought, no mind games involved in using them.
I feel like you're oversimplifying. Saying there's no thought to using a lot of traits is like saying there's no thought to using an ex move. An EX move is (almost) always better than not using the EX move, but a bar burnt here is a bar that can't be burnt later, this is the fundamental concept behind clash and meter management in general. I don't think the drawback to a trait has to be some obvious character gimping flaw, it could just be well, sometimes just the fact that he can't have the trait on all the time is gimp enough.
For example, even if your trait is just "I'm better for 10 seconds" you still need to plan and optimize that ten seconds. (Good) Superman players don't just "mash" the trait button the second it lights up, nor do Martians, Shazams, Green Lanterns or Zod's. Because if you mash trait to score the final hit of a lifebar, you've effectively wasted its benefit. And I don't think any of those characters are so "good" without them that they can afford to be wasted or thrown away. With and without trait Zod is effectively two completely different characters, and the Zod player must take full advantage of both those times to be effective.
And again, this really only addresses maybe 10 traits (not even the majority) in the whole game. Everyone else literally has to plan and integrate it into their gameplan (or is burdened with a trait that is a turkey). I think the only character who's trait has literally zero drawback is Lobo, and that kinda fits into the kind of guy Lobo is.
That was just a suggestion, I'm not saying it should be like that, it was just an idea. Because after pressing trait your opponent is already scared to touch you so should they also still be scared of all your lightning crap?
BA's trait is already "checked" by the fact that he can't simply turn it on / off whenever he wants, and it goes away if he waits too long. Taking away lighting basically makes his trait a rushdown only "stance" in exchange for I think 8% chip. It telegraphs your intentions and means if BA presses trait from full screen (when most of them activate it to close out a round / game), pure zoning characters are now free to shoot him with impunity, because his trait goes away if he does anything but block.
In any event, nitpicking your examples aside; I like to think (given they dedicated a whole button to it) the idea behind traits was to actually round out a characters movelist not simply be some additional "option" that you can probably ignore because its too risky. By design the trait "should" be as big a part of their movelist as any other punch / kick button. How much they actually achieved that goal is subject to some debate, but I don't think giving traits less utility and making them even more situational by adding more drawbacks is the right way to go.