Are you asking about using old joysticks with old games on modern systems, or modern joysticks and controls with old games?

Old Windows games used DirectInput and many new controllers are XInput, there are already way to remap these to work with old games. The PCGamingWiki page for Crimson Skies mentions XInput Plus and has instructions for setting everything up.
https://www.pcgamingwiki.com/wiki/Crimson_Skies
https://sites.google.com/site/0dd14lab/xinput-plus

Here's a video with additional tools as well that goes more in-depth along with making it work with SteamInput.
https://www.youtube.com/watch?v=1OJxQ84bZcY

Really old games use WinMM, not DirectInput.

I'm pretty sure Dege will say this is out of scope, dgVoodoo2 only handles some mouse input because the mouse cursor is rendered to screen and is dependent on screen coordinates (which dgVoodoo's rendering can alter). Gamepad controllers have no relation to rendering at all.

PCGW has a list with some useful tools:
https://www.pcgamingwiki.com/wiki/Glossary:Co … XInput_wrappers
I would recommend getting a controller that has an XInput mode, most of the tools are made for this. Though I'm sure you could get everything working with a DirectInput controller, just a bit more complicated.

I find the controller situation for old games very messy and in need of a good clean simple to use solution. Xinput Plus is great, but it isn't user friendly. But that needs to be done by someone who's knowledgable about how the gamepad inputs works and wants to do it.

Yes, unfortunately it's out of scope... It'd be nice to include other non-graphics components, sound, input, etc, to turn dgV into a more general compatibility kit...
But it needs tons of time to write and maintain them.