As far as I can tell, MLE+ doesn't use BCVTB. At least, the BCVTB gui doesn't need to be used while connecting Matlab to EnergyPlus via MLE+. Note that when I used MLE+, I had already tried using BCVTB so it was already installed on the computer.

I found MLE+ easier to use than BCVTB, which had a steeper learning curve. I think that BCVTB is probably more flexible because it can also link to other software/files than just Matlab, but if all you need is it co-simulation between EnergyPlus and Matlab scripts, then MLE+ should be easier to figure out. It's been a little while since I've used it though, so I won't be able to provide anything more specific off the top of my head.