This looks great! Also, forgive me if I repeat anything, but I think the EXE1 sprites are like that is because SS uses the same sprite style (no dark outline and similar sizes like EXE4-6 and, I think, SS1). I'm guessing that Clock Genius/Man came from the future to the EXE timeline, and Geo and Omega-Xis followed him there.
The map will help with the EXE1-era Internet, I'm sure. Needed to use maps to find my way through it anyways. And Bass should have some story, especially now that we know his backstory and all.
And more music! Maybe it'll change based on whether MegaMan.EXE or MegaMan (SS) is playing, and maybe there'll be viruses from SS in this timeline! Still, I will get this!
Also, maybe you'll get an SF Buster PowerUp in this!