I feel like Bass should win this? I've read the whole thread, and I really liked all the arguments and reasoning, and both are really sound.
I can see both winning, as they have good chances, and Proto Man does have the advantage in close range and his experience should grant him a win in any closer fight, but Bass isn't really helpless, and he can stay afar more easily than Proto Man can stay close.
Of course, Proto Man's shield can block almost all shots, but Bass's shots, at least if we take his appearance in Megaman & Bass, can be quite difficult for Proto Man to block in that regard, as in he can fire them in a much faster sequence and speed, all the while taking more unpredictable angles. With the Super Adapter and the special weapons, I lean towards Bass... But it is close. Really close.