Why does my dryer duct have such a long vertical portion?
Well first, the outlet being at-grade is a no-no for those pest reasons. They don't have to get up the vertical pipe to cause problems; a mouse or bird can nest in there and cause problems. They did it anyway because it was easier to run it down through the crawl space then up to the ceiling (where, if this is your garage, they'd then have to build a sealed bulkhead to prevent exhaust gases from your car getting into the vent line). If this is your situation I'd look at replacing the vent cap with a "critter-proof" model; there are several basic ideas, some more effective than others but all better than the single-flap standard model.

As for the vertical portion, they probably placed it high to allow for a stackable W/D. A higher placement also allows the flex vent more room to, well, flex, no matter where the dryer is. While it may seem logical to put the inlet to the vent directly behind the outlet from the dryer, doing this can actually be a pain, as the flex line then has to be fully compressed in line with the inlet and outlet, in order to avoid crushing it when the dryer is moved into place. It's really hard to get six feet of flex line to do that (and you need six feet of flex line so you can pull the dryer out enough to get behind it with the line still connected).

You can probably take out a couple feet of the rigid vent to lower the inlet. I'm not sure you'll really get more efficient venting, but it won't cause any more rodent problems than you'd already have with this setup.