I think your experience with MXM is fairly typical, and illustrates a major advantage of MVM - the latter is much easier to set up. Part of the reason is that MXM is also a Maypole frontend, not just a view. So you have to configure it with all the component roots yourself. MXM is also currently restricted to mod_perl setups, although it shouldn't be too difficult to generalise it to CGI setups. A disadvantage of MVM is that it recreates the Mason interpreter for every request. MXM keeps it around, either creating it implicitly in the first request to each Apache child, or if you call init() in your setup code, you'll get a single interpreter that gets inherited across the Apache startup fork. But the main difference is configurability. With MXM you can set up any Mason config settings in your Maypole app. An example is the in_package setting. In MVM, the Mason components run in the default Mason namespace (HTML::Mason::Commands). That's fine if you just have one Mason app on your server, or if your Mason apps are running via cgi. But if you have several Mason apps running in virtual hosts on a mod_perl server, they all need to run in their own namespace.
So I think if you're running under mod_perl, and you need to customise your Mason setup, then MXM gives you the tools, at the cost of a tricky setup if this is your first exposure to Maypole. If you want to get started quickly with Maypole, maybe just running a test setup, and you don't need to customise Mason, then go for MVM. If you're running under CGI, go for MVM. If you're running under CGI, but want a customised Mason setup, then you're on your own. Either patch MVM to accept Mason settings, or patch MXM to run under CGI.
p.s. I think you're wrong about the autohandlers/dhandlers. These should work fine with MVM. I think the templates included with MVM use the headers/footers because they were ported from the TT templates in Maypole. You could use the MXM templates with MVM and they should work fine, and they include an autohandler that brings in the headers/footers.
p.p.s. the author of MVM disagrees with a few design decisions I made in MXM. These may well affect your choice. Unfortunately the mailing list archives are down at the moment, but you'll be able to find the message in there announcing version 0.3 of MVM.