I have to go to the beginning of the thread to see if I can add anything substantive that has not been said already.
However, I can provide a few basic thoughts on vert vs. hori shoot-em-ups:
1. I love both, but, echoing Black_Tiger, I think of vert and hori as two distinct subgenres.
2. From a design aspect, I think it is EASIER to create a mediocre vertical game... the mechanics and gameplay formulas just seem easier to implement. When I was a kid, I created a basic vert shoot-em-up for the Apple II and it actually was kinda fun to play (it was a bit choppy, though). For whatever reasons, I had a much more difficult time making a horizontal shoot-em-up that was actually fun to play. I am talking about pure mechanics here, since both games were aesthetic equivalents and had "polished graphics" (courtesy my brother!). As a result, I have more respect for a well-executed horizontal shooter. Call me crazy.
3. There are exemplary titles in both subgenres, so I have no preference. They each provide good times. But, if you take #2 above to heart, I have soft-spot for well-made horizontals. ALTERNATIVELY, I have lower standards for verticals. See? I don't know.
4. Thunder Force II, though, defies #2. The "vertical" stages are lame. I appreciate what Technosoft was trying to do, but the execution had a lot to be desired. The horizontal stages were clearly the game's strong point.
5. MegaZone (Konami) Rules!
6. See number 5.