There are two issues with this so far.

The first is that the baseline easily gets out of sync as soon as we update a client application with customizations. It becomes very difficult to roll enhancements back into the base and to roll enhancements from the base back out to our clients.  I don’t have a solution for this yet outside of being meticulous about using a number Design Patterns to help prevent too many dependencies among components.  I also don’t have time to sync code among clients and baseline, so the more we code the more out of sync it gets.  I need to allocate time just to sync the packages, which is counterintuitive with the idea that this is supposed to save time.

The second issue is that we just became resellers for Telerik RAD Controls (announcements to be made soon but you read it here first!) and while I’d like to incorporate these controls into the package there will be some sites that don’t want to use them.  So this means we’ll need two different packages.  There are a lot of algorithms that don’t involve the UI, like the MV Membership Provider, but the Master Pages, Themes, and anything else related to Ajax all work differently.  In short, you can easily "ajaxify" non-ajax code with the controls, but you can’t "unajaxify" RAD Controls for an environment that doesn’t want them.

That’s where we stand now. Thanks for asking about this guys. I’ll update here if anything changes.