Either is perfectly acceptable. If you don't want to see armored running down your wall, you could also mount a box up above and transition from armored to EMT at that box. If it's a short run of EMT just down the wall, you could even do it without a splice, just strip the armor off the last several feet, and leave a service loop in the box in case you ever want or need to cut and splice later.
I have armored running thru the rafters in my own barn, for most of the lighting, but only ever use EMT when running on the wall in a finished shop space.
Make sure you know which cable clamps to use with armored cable, they're not the same as NM-B (Romex) clamps, and make sure you know how to terminate the sheathing so it won't chafe the wiring. But there's nothing wrong with armor, other than cosmetics.
