I'll go with the Master being an alien (but still human), myself.
I've spent two days lurking around Angelfire, after finding out that it had a search function (something Tripod doesn't seem to have. One point for Angelfire!). My goal? To find as much old Megaman stuff as possible, be it minor or major. (Which, admittedly, is less "theories" as it is "they didn't even care when they wrote this") Turns out there was a lot of interesting material there, amongst all the RPGs that weren't updated since the day they went up and horribly designed pages, the only purpose of which seemed to be to murder my eyes.
http://angelfire.com/theforce2/megaman/ - Claims Protoman was brainwashed by Dr. Wily.
http://mmxz.zophar.net/ - Not on Angelfire, but found though it. Apparently confuses Protoman's personality with Bass's.
http://angelfire.com/wv/sOnIc/mm.html - Bungles the plots of MM3-6 and 8 (slightly; "EVIL" wasn't really a spirit). Would you have ever guessed that Protoman was the Big Bad of MM6?
Quoted in case the site ever goes kaput:
Megaman III - NES, Game Boy, PC
Not again. Dr. Wily doesn't know when to give up. Can Megaman defeat him again, This time, Megaman will have a little help from his new dog, Rush, and his best friend, Roll.
Megaman IV - NES, Game Boy
Will Dr. Wily ever give up or is he going to create these robots till the end of time? Megaman must go defeat even harder robots like Toad Man and Dive Man and Skull Man and make the world a safer place.
Megaman V - NES, Game Boy
Dr. Wily has created a brother for Megaman named Protoman. Sometimes, Protoman will help Megaman. Others, he will try to defeat Megaman as much as possible. Can Megaman defeat both Protoman and Dr. Wily?
Megaman VI - NES
Dr. Wily strikes again, and so does Protoman. But, Megaman has more help this time. Megaman will use Beat, his pet bird, to get to places and use Rush as super armor.
http://angelfire.com/mb/megaman1/ - Confuses Megaman with X. Lots of horrible low-res pics and animated sprites on crack.
http://angelfire.com/mo/giants/ - Mentions Metool's Megaman Rockworld, Mega Boy's Megaman Homepage, and Realm of Megaman X--all defunct.
http://angelfire.com/ultra/megamanworld/ - Has a page devoted to the RM3/MM3 prototype.
http://angelfire.com/ult/ace/batton.html - Details the creation of a newsprint Battonton; there's more on the site itself.
http://angelfire.com/ex/megazero/ - Claims X is Mega, without giving any evidence. (Something quite a few people on Angelfire did, actually. Megaman-is-X, supergifs, and grainy official art were all recurring themes)
http://angelfire.com/dragon/megamanbass/ - Devoted to Megaman and Bass; refers to King as "King Robot".
http://angelfire.com/games/calc/mm.txt - Description of a calculator fangame.
http://angelfire.com/games/megaman1/infopage.html - Says Protoman "vanished in an accident" and was "tricked" by Dr. Wily (Wily didn't trick him; Proto was just grateful). Also uses a pic of Volnutt in reference to the original Megaman (which Cannon Spike also did...).
http://angelfire.com/games5/gizmonics/ - "Megaman X Nightmare" demo; the link to the demo doesn't work.
http://angelfire.com/nt/okenet/rockdata.html - Uses Megamix pixel art; their data is off. Just read Elecman's bio.
http://angelfire.com/games3/mmx0/comics.html - Contains info on the series up to Zero. (Only once did I see ZX mentioned on all of Angelfire)
http://angelfire.com/biz4/t87megaman/index.html - Vile X Lab. Closed.
http://angelfire.com/comics/mmo3/ - A fan comic with original designs.
http://angelfire.com/anime5/megaman-zero-project/ - Creates a factless story about Protoman's presence in the X series. (I don't remember if it was a fanfic-oriented site or giving the "facts")
http://angelfire.com/comics/tamm/ - A strange sprite comic with awful grammar.
http://angelfire.com/falcon/favoritestuff/ - Arbitrarily connects Ruby-Spears Megaman with Astro Boy. (OK, Classic I could understand...but RUBY-SPEARS?!)
http://angelfire.com/rpg2/megamanultama/ - Contains a few fangames. (I didn't test them to see if they still worked)
http://angelfire.com/hero/protozero/ - An odd sprite comic; plot feels very DBZ-ish, from what I read of it.
http://angelfire.com/anime5/thelair/mmarchive.html - Detailed site; includes info on the Jazwares figure and the Ruby-Spears production (which is really just his two cents on both matters, but no one else was talking about them...)
http://angelfire.com/games3/megamanX/ - Claims Protoman was the Big Bad of MM4. (I can't get the link to work, so don't bother with it. You'll just get 404'd.)
http://angelfire.com/me4/fanworks/mfw/main.html - Contains a translation of the X5 manga (no scans, just text).
All in all, I've got a slightly better idea of what the fandom looked like back then...at least on Angelfire. (R.I.P., Geocities) Whaddya think? (By the way, I wouldn't have touched this thread again if Vixy hadn't said it was all right. Thank you
)