As a preference I'd have to go with horizontal. I do love some vertical ones (Raiden series mainly, also Gunbird and Trigon) but R-Type, Chronos, Thundercross II, Progear are so much more fun.
In the overhead view used in vertical scrollers you typically don't have scenery to work around (Xenon II is the only one that springs to mind that does that well in the vertical). Instead they just go overboard and add stupid amounts of bullets. Where there are obstructions, like in Varth, they can be very hard to pick out from the other scenic details. With the side-on view of the horizontal scroller, solid scenery makes things much more interesting. Though it's really about that overhead view. A horizontal scroller with an overhead view (like Uridium) suffers from the same irritations as those vertical scrollers.
One thing I really don't like is vertical shooters with a horizontally-oriented screen. A lot of vertical-oriented screen shooters do scroll a little left and right, but enemies that are off the screen don't tend to shoot at you. With a wider screen, there are lots of lazy ways for the developer to throw in enemies from both sides at once or the top corners of the screen where you can't get them all before they hit you. Lightforce, the vertical stages of Salamander, and when the Aero Fighters series switched platforms and any other vertical shooters for the Neo Geo hardware all suffer badly.