In Act 1 Megaman is missing his ironic Mega Manning ability, or so it seems. During all of act 1 the only named robot he defeats is Protoman, after which he adopts the same view point and forsakes mankind just like Protoman did. Copying his views not his powers.
Why does the Heartbeat Soundtrack start as the same time as the synths in Act II? Because it's when Joe's born!
In the games, the Sniper Joe robot was based on Protoman. The Sniper robot explains how Light got materials to make Protoman in Act I.
In "Funeral For a Son", why were the people whispering of Protoman? Because he was alive, working for Wily, and oppressing them!
Remember Light and Wily's argument back in The Good Doctor? Most people assume that it was Wily who ultimately won the argument, as the entire first album shows. But that's not true, when you think about it enough. Light was right: there was still one man courageous enough to stand up against Wily's oppression.