Can I animate a mesh using raw vertex coordinates per frame? I'm interested in creating an animation in Blender that involves an intricate and roughly-scientifically-accurate animation, that appears to be beyond the ability of Blender to perform easily and accurately. This animation will be mixed with other animations in the same scene that will be done using standard keyframing/rigging.

As a result, I'd like to write a program that generates mesh data for each frame and outputs it in some format (likely X,Y,Z, and a few texture parameters for cycles, perhaps U/V for a UV map). Is there a way to easily import this bulk mesh data into Blender so that I can obtain an animated object, without importing a separate mesh per frame?
I would suggest writing to an Alembic file. Blender has nice support for it, and it's a quite compact file format that's fast to read. It also supports things like changes in mesh topology, vertex colours, and point clouds.