In an earlier post, I explained my concerns with transparent system-wide persistence. One of the problems I pointed out, is that in such a system, you have to manually serialize all important state on upgrades and in some other situations anyways, relativating the value of transparent persistence.
Marcus Brinkmann now showed me a nice text explaining the upgrade problem in great detail. It's a good read, at least the first half.
BTW, meanwhile I refined some of the ideas I tried to explain in the original discussion, and I might post an upgrade at some point; but all in all, my concerns with transparent system-wide persistence haven't changed.