Dialed in some more stuff on my Boss GT1000 Core that I just got. Apparently, the dividers/mixers, even if you aren't using them, affect the volume/sound. Not particularly fond of that, but it is good to know. The various volumes are a bit excessive (send/return for the loops, which I use for my Syn-2 preamps, the system level on the face of the device, the patch level, direct levels on every effect, etc). Some of this was present on the MS-3. The stuff that wasn't just requires experimentation and going with what sounds best.
What I really like is that you can save effects as stompboxes. That's pretty useful if you plan to use certain effects settings, or close to it, such as using the dual delay on a bunch of patches, but just change the time of the delays. Definitely enjoying the latency, as it is pretty unnoticeable.