There is a difference between "super-strong" and "unkillable".
In Metroid Fusion, there is a recurring enemy called a "SA-X" that can kill you in only a few hits. Normally, you are expected to simply run away.
You find out late in the game that there are several SA-X roaming around searching for you.
(Ironically, any SA-X you encounter disappear if you leave the room)
The final battle of the game (for those aware of the ending, the final final battle doesn't really count as a battle per say) is between you and a single SA-X.
Before this point, every SA-X you encountered in the game was unkillable.
The given reason why this was the final battle was because YOU finally acquired enough generic firepower to fight against a SA-X.
At no point did some plot-driven event effect your ability to kill the SA-X. At no point in the game did you ascend to some "higher plane" that enabled you to challenge a SA-X. At no point did you weaken the SA-X during the battle, enabling you to fight it as you are. At no point did you acquire a superweapon enabling you to penetrate their defenses. At no point did the SA-X run away if you damaged it enough. The final battle only happened when it did because you had gained suffecient generic firepower.
Under that pretense, you should of been able to kill any other SA-X in the game if you were just that good a player.
To the dev team's credit, you were always capable of "damaging" the SA-X in previous encounters, but it only stunned them for a split second. You never actually damaged them, regardless of how much skill you had.
This might of been realistically acceptable if there was only ever one SA-X, (and therefore would of been plot-breaking to kill it) but there weren't. There were like... 10 of them roaming around, allegedly. (Your boss in the game could of lied about the number, but there had to of been at least two SA-X as there's an event in the game where one "had" to of died... unless it escaped, in which case there could of been only ever one SA-X)
They could of accomodated for this design flaw by allowing you the kill the SA-X and revealing that there's more than one next time a SA-X had to be mentioned.
In any case, unless killing a recurring boss requires you to drastically alter the playing field (such as by ascending to a higher plane, weakening the enemy, or acquiring a superweapon) never make that recurring boss unkillable, especially if killing it wouldn't irreparably break the game.
In Chrono Trigger, there is a point in the game where you face off against the final boss early. However, the first thing that happens in the battle is an attack which does enough damage to usually kill you. (this defeat is part of a plot device, and does not end the game) However, if you were levelled up enough (i.e. suffeciently skilled) you could live through the attack and go on to beat the game early.
Chrono Trigger was made over 10 years ago and they understood this. We have no excuse.