I've painted both. The thing that I like about clear is that if you get a light parking lot scrape or fine scratches, you can sand/buff the clear down (assuming you layer enough on) and not touch the color. As long as you clean it well, you can reshoot clear w/o a lot of concern over the matching (obviously, its clear). sags and runs are a little easier to miss on clear unless it is super bright where you are painting. the other thing that i noticed on my jeep (base/clear) was that if you get dirt/dust/bugs in the clear, they stand out more than if they are in just a color shot (get covered with paint) I have a small gnat that is encased in clear on the lower rear of my jeep's front fender. Kinda jurassic park style. but its low and usually covered in mud so i don't worry about it.
Some of you guys who have much more experience painting may disagree (please do!!) but its all about prepwork. any shortcuts on bodywork/primer will be magnified exponentially after the paint is on. work clean, easy light coats, READ THE LABEL to know what/how to apply/reduce/harden/etc.
Sorry I'm long winded tonight.
