I'm gonna make one suggestion. USB.
USB is a standard introduced in the mid-late 1990's, and is incredibly ubiquitous to this day. If you can, in any way, get something to function over USB, even if it's just using an RS-232 serial emulator, which are also incredibly ubiquitous (Heck, even RS-232 might not be a bad idea) use it.
There exist few computers on the market without USB support, and I imagine it's going to be around long enough to make future replacements of any peripherals or main systems a lot easier.
As for the basis of what machine to use, use x86. It's been around in the IBM PC compatible basis since 1981, and will NEVER be hard to come by until decades after it's death. If you are looking for a robust route to go, with ease of finding replacement parts in the future, x86, and USB. Those two will not die for a long time.