If defeating a Gigantix, is (as you say) a "rare accomplishment", than the loot it drops should reflect it. Instead, it drops capsules and 4* just like any other grindable content in the game. If SEGA intended them to not be killed often, it stands to reason that their loot would reflect it more; with higher % of II capsules and better loot than what we've already been able to get now.
They don't, so they're not meant to be. If Challenge is the problem though, you can tailor the difficulty of the fight entirely to your own specifications, by fighting them solo.