Thank you all for your input. I actually got the game saving and loading properly in Kega Fusion, which I prefer over Gens. While I would have liked to play it on Regen Dev build with the overclocking, which I tested and it worked flawlessly, the slowdown isn't that big of a deal and, to be honest, sometimes it helps old relics like me with less than stellar reflexes.
I saw on a forum somewhere that SRAM support for games was being handled on a case-by-case basis by the developer, and my conclusion is that Wily Wars was never take into account. While the game definitely creates the .srm file in the player-specified directory, it's either fault or isn't loaded when the game is started. Regen has been abandoned for years, so I'm going to have to give up on this one.
I would look into the Japanese version, but I wouldn't be able to use the Flow patch with it, which I really enjoy, so I don't think that I will. I have actually looked at RetroArch, but I've found that the menus and interface are very difficult to work with. I suppose that I'm not patient enough right now to untangle everything.