I just picked up a mc6. Glad I went for the extra switches over smaller hardware. And with the recent announcement mc6 will be able to do trs output to your Jackson (when you get it) via one of the inputs. So yeah I vote mc6.
I think it’s not so much future-proofing with the MC6 but rather it really depends on how many switches you need. If you can get by with having access to 3 presets per bank for scrolling etc, or even if you just need access to Start, Stop and Play for a Looper function, the MC3 will do the job just fine.