I actually had this debate with my wife when my first box of UGCs came in. At first I was all for keeping everything (N64 included) as close to retail as possible, but there are a TON of really bad horizontal covers. My wife talked me into using vertical covers (and everyone I asked opinions from agreed that they looked better), so I went that route and never looked back. They look FANTASTIC, and it makes me feel like I have the equivalent of a rental library in my house. Very professional looking.
At this point, even if a more unified horizontal system was established, I would probably stay the course with verticals. Not only have I come to enjoy their look more than retail horizontals, but my entire collection has already been printed in the vertical format and I have no desire to re-print 100+ different covers.