I always bought matte finishes. The nook classic had a shiny frame and I would pick up an occassional glare in bright light. The dark matte finish resolved this issue.
I've never used a skin on my nooks. They are kept in javoedge covers that protect them very well and cover almost all exposed surfaces (but the screen of course *grin*). My kids just got 3ds and we got them skins for those devices. My son's is shiny and my daughter's is matte. I like the feel of the shiny one better to hold, but I like the look of the matte one.