I just had to respond on this one... 
I started using Bootstrap by adding it manually to every database. As David mentioned: a real pain for things like dialogs. That was also why I started writing up everything I learned at bootstrap4xpages.com. The plugin makes my life a lot easier. With the custom renderers it's simply much easier to work with in an XPages environment. My advice would definitely be:
go with the plugin. Besides the built-in integration with XPages that gives you benefits like an easy install in every application, shared resources, built-in resource aggregation and more. Although you could use it without much knowledge of Bootstrap, I'd still recommend to go to
getbootstrap.com and read the documentation (the same goes if you're using OneUI): if you're building web apps you'll need to know what's going on under the hood. Oh, and if you don't want to use the Application Layout you can always create your own layout control.
About keeping current: the plugin currently contains the latest Bootstrap release (v3.1.1). My plan is for the foreseeable future to keep embedding updates. I heard from 2 (new) people in the past two weeks that they want to contribute, so I'm hoping we'll get more help. Setting up a good dev environment is complex, I agree with that, but that's not specific to the Bootstrap4XPages plugin: it goes for all OSGi plugin development for Domino. There are excellent resources available to help you with that (like this slidedeck by David Taieb
http://www.slideshare.net/fiorep/domino-osgi-development and this webcast by Phil Riand
https://www.youtube.com/watch?v=uAff5uNwhn0).
I agree that the documentation is limited. Unfortunately I haven't been able to contribute much on that part. Would love to have people help us out. That doesn't mean there isn't anything available: the webcast above, the slidedeck from our session at Connect and the session I did at Engage 2014. On June 17th I will also do a webcast (together with TLCC/ Teamstudio) on Bootstrap4XPages. For the next release of the plugin we've also planned to include a demo database.
(BTW: I stopped adding Bootstrap to every application and now use the Bootstrap4XPages plugin in all new projects. The
bootstrap4xpages.com site has also been converted)