Despite publishing in PLoS journals a fair amount, I'm not a huge fan of the actual customer experience of publishing on their platform. I once seriously gave up first authorship on a paper in exchange for not having to deal with PLoS Currents' submission system.
Similarly, the BMC-system appears to be having serious issues with turning around papers swiftly enough.
Of course you're right, but the review process is connected to the journal. PLoS journals are very accepting and so they end up being seen as a repository for publications that could not get published elsewhere. That's not to say nothing of value is published there, but rather that if you take a random paper from one of their journals, it's going to be of a different quality than a random paper from the Annual Review of Astronomy and Astrophysics.
And like others have mentioned, a supplement is a great idea because of publication bias against things like negative results. However, I would again see this as supplementing and supplanting when I think most people here are gunning for the latter.
Similarly, the BMC-system appears to be having serious issues with turning around papers swiftly enough.