Nathan is right that I am contradicting myself a bit. It's true that if you don't look at the interwiki map, you'll never know what's there - you'll never know that WMF is stuffing the default map full of its own junk. What I really meant to say is that external users will feel short-changed that we get to add "our" internal interwikis to the global map, yet they aren't allowed to add their internal wikis (equivalent to our strategy, outreach, etc) to the global map, for any given reason.
I'm not getting a coherent sense of a direction to take. Do we split the existing interwiki map into a local and a global map (as I originally proposed)? Do we start from scratch, rewriting the interwiki map from a blank slate, or do we start with what we've got? Do we flood external MW users with a ton of new prefixes, or do we ship a mostly empty table to new MW installations? Do we scale right back and limit ourselves to a small core of interwiki prefixes? Do we take up Tim's idea and toss interwikis altogether?