At the arcade I work at, we plan on taking the oneswitch.org.uk approach. I'll detail it here in case it's useful to you.

A standard already exists to provide alternative inputs - it's very simple, just 3.5mm mono sockets. Like headphone sockets, you see. Cheap, ubiquitous, easy to wire in. Because everyone's disability is different, trying to cater to all different abilities would be a monumental task that we would likely fail - oneswitch's philosophy is that the manufacturer should provide a standardized alternative input method, and the people who use them would sort out their own human-facing interface that's suited to their particular needs.

So, an interface for a pinball machine could take two forms - on a dedicated machine, simply drill a pair of holes in the underside of the cab where they won't degrade the value too much, and run wires in parallel with flipper logic there. On older games where the flipper switches drive the flippers directly, transistors or solid-state relays can be used.

The second form would be one that could be transported around other machines, like Ben Heck has made - except one that would operate both flippers, and instead of having buttons, it'd have a pair of 3.5mm sockets into which the player could plug their own interface. That could be a box with buttons, or a pair of foot pedals, or eyeblink detectors, whatever works for them.

I hope this is useful! You might find inspiration also at oneswitch.org.uk.