"Minecraft Community" is a slight misnomer, in practice Minecraft players are fragmented into a large number of different communities.
While there are lots of splits between different play styles (RP, PvP, PvE, etc) - the real point of division is between those using the Official server, CraftBukkit, Spout, Forge, and any other number of 3rd party modifications and servers. And this causes a number of problems:
First is the issue that all server administrators are familiar with whereby mods can take considerable time to be updated after the release of the official server. This means frustrated players who want to use new features or see other improvements and bug fixes. The demand from players pushes server admins to use buggy and unstable versions of mods that aren't ready yet. Worse yet, the demand from server admins on the mod developers to get things done quickly runs a higher risk of lower quality code.
Having the large majority of people using a single, stable, and centrally managed API sidesteps all of this. Of course 3rd party mods are pretty unlikely to disappear entirely, but with any luck they will be the exception - not the norm.
Being locked into a single mod
If you've set up a server and a community around a particular mod, switching from that is a lot of effort. At the very least you've got to find equivalent plugins to keep all of your existing functionality, and at the worst you end up with less than you started off with. Having all extra functionality implemented as plugins instead of as a completely different flavor of the server prevents this entirely, allowing you to swap out functionality much more easily.
Fragmentation of skill
The fragmentation within the community means that the skill pool available for interesting new plugins is divided, since developers on the large prefer to write plugins for a single mod. By having everyone on the same book, there will hopefully be a greater number of high quality plugins available.
Dwindling interest in the game
It's been a long time since Minecraft has had any kind of 'major' development - and while the modding community has managed to largely keep the ball rolling, it only has so much momentum but its effectiveness is dimished by a fragmented community. If you're starting a new public server, building up a decent sized and regular community is a challenge. Major new functionality with lots of potential rekindles interest and gets people playing again.
It's not all sunshine and roses though, the community is going to have a set of interesting challenges in its way, which I shall detail in a separate article.