I'm guilty of complaining about a feature lacking in Domain Mapping. One issue that has hanging around in both domain mapping plugins is the problem of Ajax implementation. On a mapped site, ajax doesn't work. You can get it to work by disabling remote login when using the repository plugin, you can't get it to work using the WPMU DEV plugin.
I've made a lot of complaints about it on these forums:
Anyhow, I recently saw an update to a thread that Aaron start a few months back on the Wordpress.org forums: http://wordpress.org/support/topic/dont-redirect-admin-ajax
There is a comment about trying out the development version of the repository plugin. The fix turned out to be only 4 lines of code added to the plugin. the dev version is 0.5.4.2. Ajax now works with remote login enabled.
I installed the dev version last week and tested it out. I have remote login enabled for it so logged in users are passed through no matter where they navigate to on the network.
Now, the point of this post....
The noted version of the repository plugin fixes the ajax issue and now you get the best of both worlds. I now have MarketPress network-wide (which uses ajax heavily for the shopping cart - a core function) installed and working on a multisite network that supports global login and domain mapping.
I do believe that this one little fix turns a Multisite+MarketPress installation into a potential commercial monster! This fix lets you create full and independent e-commerce websites, on the network (taking advantage of marketpress' unique network features) with all the moving parts functioning correctly!
This was a big hurdle for me and am pleased that a solution was found!