I think that if you try to restrict it too much, you lose the allure of the cup. However, if you leave the doors wide open then you'll just get HAL9000 driving the boats which isn't something that we want either.
I think that the way the next cup should works is that when teams sign up and put down their entry fee, they get a "template boat". Not a design... not a set of plans, but an actual BOAT. If you want a second one, then you can buy a second one but no more than two (unless you destroy one of them)
From that point forwards, the rules allow you to make modifications to that boat to a certain limit.
What this means is that the playing field is more level. The major design costs would be manageable and you'd basically all be starting on square 1 in terms of build/design/technology.