NECROPOST! Two and a half years later .... KABOOM. All the Bukkit staff have resigned, Wesley Wolfe's DMCA has taken down Bukkit, Spigot and Cauldron, and Mojang don't have any real motivation to help fix the disaster they helped precipitate.
I won't summarise, there's a lot to be found elsewhere (spigot forum is particularly good).
Bukkit looks to be *really* dead this time.
The upshot, however, is far more interesting: it seems to have driven everyone who cares - devs, bukkit staff, forge team and modders, and server owners - to get together and build a replacement. They want to call it Sponge, and it already has a stub website (spongepowered.org). It would be interesting to get in on the ground level. Anyone who still reads here interested? Visit the site, it links to their google design doc. Then head to #sponge on espernet, it's bustling.
Time will tell if this sticks, but it's a very promising start to a new and improved API and MC server wrapper.
Oh, and we still love ya Drakia, even if MC gives you PTSD. Stargate *still* works