Custom key mapping and joypad support is planned which should wipe out the rollover problem. What would be a working default key config to avoid rollover and give a pleasing input scheme? IMO WASD for movement and keys like SHIFT or CTRL should work on most machines.
In my game project I use WSAD for movement and aim/fire with the mouse. Since this game is made differently possibly try these buttons but your main firing keys be J and K. I use this to avoid rollover for my Megadrive emulator when using it on older PCs.
The only concern with hardware-acceleration vs. software emulation are supported resolutions. Due to my non-sprite-scaling policy I'm bound to the lowest supported resolution. Many professional indie games don't offer resolutions below 1024x768 these days, even when they are aimed on low specs. Therefore I will use 1024x768 as minimum. Higher resolutions either won't be supported or just have a broader GUI. The play field will stay the same size. Damned, 3D would be so much easier here.
1024x768 is about as far as I'd go with older machines - I refuse to set it to 1280x1024, it just has no benefit for the machine of its age. I do believe most Doujin games use the GUI extending technique (which is annoying for me personally but would work in this case), so I got no arguments with using that to solve the higher res issue.
As for 3D, while being a good idea would essentially defeat the purpose of this discussion with older PCs as such 3D implementation would be completely unrunnable on machines of the older era which I've discussed.