I really like Soul K's suggestion re buying protection ... given a decent amount of notice to earn the creds required (say a month), I think it would be quite fair and would provide a good balance between protection of active and historically important builds, and renewal of the map.
I'm quite excited about the whole idea. I have around 6 key realms that I will be saving (my vault, skelly grinder, gold farm and sugarcane farm) but will be happy to see the other 80 realms wiped clean, even those which I have done quite a bit of work on. The main thing I would want is a good bit of notice so that I could remove my materials from those realms.
I would love to see the nether wiped at the same time too, if possible. Part of the excitement of MineRealm is the community spirit (remember excavating Intelli's, Torn's and Rokkr's spawn realms?) and I feel that has dwindled since so many players and areas have neared end-game conditions.
I don't think it would be a bad thing to lose the subway say ... it would give opportunity to build something new and better, maybe an aerial railway that actually shows off MineRealm rather than tunnelling through beneath it, or a gridded network of nether rails that provides access to almost the entire map. The possibilities are endless
