This is really not any different than what's been happening for years now...

Let me paint a picture...

Every new version of WordPress that comes out is promptly followed by a supplemental version of WordPressMU, which introduces all of the new .ORG changes into MU. All that will eventually happen, is that .ORG and MU will join up and have 1 installation that asks "Would you like one blog, or many blogs." And I suspect the answer to this question isn't permanent, considering it's totally possible to install WPMU and only have 1 blog.

So maybe "merging" isn't the right word to use when talking to developers that want to know how it's going to impact them. The answer is that it really won't. The audience that just wants one blog will continue to have the same plugins working the same way they do now. Users wanting a community with more than one blog will want to use plugins that focus on the USER on the SITE versus the BLOG, just like BuddyPress does.

Really, as soon as the 2.8 changes make it into WPMU, I suspect that wordpress.org code will just turn into MU code, but still be called .org.

Clear as mud? Haha! This is all just my speculation at this point, but I think from a developmental standpoint this makes sense, and would even make sense if you were looking at this from a long term perspective...

Branch apart MU, to figure out a way to make one WordPress installation support many blogs. Okay, got it pretty well mature and figured out. Now, merge it back in and have the new more intelligent code replace the old stuff. Done.

Then again, dogs and cats could be living together, and this could be mass hysteria; I really have no idea. :)