Nanomachines/Mysterious Power seem to cost what they're worth to me. Reducing hardpoints for the Supers aren't limiting them all that much. Plus free hardpoint you don't even need to pay upgrades for. Supers already get plenty of upgrades that offer the equivalent of a hardpoint, such as extra spirits, flight, reactor and so on. Ideally, yes, you use the upgrades for those and keep the hardpoint for an advantage you cannot get otherwise. Or to save on some upgrade points at least until you get more upgrade points to spend on those.
Hard hitters being slow makes about as much sense as slow tanks. Bigass motherships/deathstar creeping in and shooting the doom laser.
Something that may make sense is for the big ones and similar single pick options (maybe not all of them, though) would be to have them get a toggle.
In the case of the slower damage-dealer, he could go around at normal speed until he activates the higher damage. The action to toggle could be significant enough to discourage using it freely, so a mecha could ride around normally until there is a fight and then switch to damage... but if the targets move around he has a hard time positioning himself strategically. Not being to toggle for a while could make more sense for those options that cannot really be reversed from so easily anyway, such as suddenly losing half your spirit points/hit points/energy. Still, just an idea.
... then what's the point? You're a sitting duck unless you only took just enough damage to heal out of it.
Aye, the first thought when seeing that upgrade was then, indeed, it actually gets you back into the fight if you heal enough to recover, kind of like DR allows you to survive the way healings normally don't. By itself it is already pretty nice. And even if your mecha cannot be back into the action for a few turns, it does indeed forces the attacker to pay attention to your mecha instead of other stuff, potentially wasting actions that are sorely needed to get rid of those that can still kick its ass. And even then he cannot fully ignore in case you get back in the fight. Strategically it is pretty useful.
If you leave the mecha, that's another target he may have to worry about, and even if the mecha doesn't get back up in time to continue the fight before it ends, you at least get to keep the same mecha for the next encounters. Better than the lower level replacement.