Would appreciate a source since you have done your research though.
Definitely Fateful Showdown and Showdown of Destiny.
I would assume anyone with basic critical thinking/common sense can figure it out fairly easily, especially an old time gamer exposed to mass amount of cliche titles/plot:
The fateful showdown between xxx/The showdown of destiny between xxx, finally after this and that long of a time...
Fate of confrontation/destiny of showdown just sounds awkward themselves or as a title.
Now I am more curious about the source of your 'research' after googling and found nothing phrased as megaman fate of confrontation/destiny of showdown
Interesting way to increase post count though