Pick however feels most comfortable to you, but here's the logic behind picking with the fingers...

A couple of physics truths to start us out: The smaller the load to be moved, the smaller the effort force needed to move the load, and the smaller the distance the load needs to be moved, the smaller the effort force needed to move that load.

Therefore...
(1) When picking from the wrist, you must move the entire hand to move the pick. The hand is more massive than the fingers (duh) so it takes more force to move it, and you're wasting energy since only the pick needs to be moved, not your whole hand. Picking using the fingers uses the smallest amount of motion and conserves energy.
(2) Keep the pick as close to the strings as possible. If you pick a downstroke on the high e string and the pick goes 4 millimeters through the string, you have to move the pick 4 millimeters back to the string, whereas if you moved the pick only 1 millimeter through the string, you'd expend only 25% of the effort as before to get it back to the string (4 times easier).

If you pick by kind of wiggling your fingers, it's hard at first since the muscles aren't used to working that way, but it uses way less energy. Now, by extending your index finger a certain amount you can move the pick up or down a few millimeters, but this won't work for heavy duty string skipping. If I need to quickly skip strings I use the wrist to reposition my fingers, and if I'm just playing a lazy passage or improvising I move my entire forearm up or down to reposition my hand. It's all about economy of motion. I used to play with only my wrist, but I find that playing with the fingers is much less stressful on my hand and I can play a lot longer at high speeds this way. Hope that helped ;)