It's about the same either way, but there are a few sweet spots that are the most useful. So it's really a choice between: leaving it completely open-ended, and people really have to know why they may need to change it in order to change it to a useful value; giving the most useful values; or do both, and hope it doesn't confuse and/or break people. I also know we'd find several MTUs of 1337 if it were free-form. ;-)
I would pick a few common values, and document why they should be used:
9000* - 6in4 over a jumbo-frame capable network.
4450* - 6in4 over a 4470 byte MTU network (Packet Over SONET)
1480 - 6in4 over a 1500 byte MTU network (FIOS, Cable Modem)
1472 - 6in4 over PPPoE over a 1500 byte network (DSL)
1280 - IPv6 Minimum MTU (Should work everywhere)
* Note, these values require your ISP to have a jumbo frame clean path to Hurricane Electric, which generally means private peering with Hurricane and configuring the peering for jumbo frames.
Then, if you wan to score bonus points, create a small tool/applet that tests the IPv4 path between the tunnel endpoint and the tunnel broker server to determine the largest IPv4 packet that can pass without fragmentation, and then make a recommendation to the user.