Remember megaman X5 and X6

I find it extremely hard to believe that Dynamo is based off Protoman, or any other Mega Man character for that matter.

Besides, didn't the ending for Protoman in PF2 explain that he had some kind of energy imbalance problem that was going to kill him?

Yes, but Dr. Light said "If he isn't fixed soon."

For all we know Dr. Cain might have serverly upgraded him if or when he went offline.

Before Dr.Cain developed reploids in the X era, he was an archaeologist who discovered the remains of many reploid battles in the original series. He found megaman and made a giant reploid culture made based on Megaman's design.

In the quote that Dynamo said in the Megaman X games however, he mentioned" I am the coolest and wisest of all", boasting about his theoretical years of experience of fighting and being wise thus proving he has lived a very very long time.