FMQ notwithstanding, there is one place a vertical bobbin is easier to deal with:
If you get a rather majestic birds' nest and the machine freezes, most of the time you can get at the threads by pulling out a vertical bobbin, snipping the threads you can reach, then removing the quilt. Drop ins with that kind of snag can be a bear to deal with.
I've used both types and prefer the vertical. The Brother 1500 and the Juki 2010 are both vertical. So is my Pfaff 2170.