#1
I've come to the conclusion that using "economy picking" or picking in the direction of a string change is really hurting me. This was just the natural way I played from the start. I've been trying to practice strict alternate picking by going really slow through things I had previously economy picked. It wasn't working out that well.

Tonight I started alternate picking arpeggios that I would normally practice with sweep picking. I started with 3 string patterns and then moved to 5 string patterns using alternate picking. It was unusually easy to do and maintain a strict alternate picking pattern. I noticed that it carried over to everything else as well. Even when going very fast (for me), I still alternate picked. It was one of those light bulb moments. In a matter of a few minutes my playing felt much smoother and my timing felt much better.

Just a suggestion for anyone in a similar situation who might be looking for something to help out.
#2
I've had the same problem, when changing from economy to alternate picking.
I advise you not to practice too much right after changing you technique. Slowly get used to it. I made the experience what happens if you don't (My hand started cracking, with every move!)

What helps to get into the feeling of alternate picking is to sit down without a guitar and imagine that you play a scale with alternate picking.

A good exercise is Snow hey ho, by the Red Hot Chili Peppers
#3
When I learned alternate picking I used the exercises in the first "monster lick" of Michael Angelo Batio's "Speed Kills". Really helped me.
I practised them really slowly and as I performed each pick stroke I would say either "down" or "up" depending on which it should be - this helped me keep track of things and make sure I was using the correct strokes; eventually it became habit.
Speed is a by-product of shut the fuck up.
#4
But guys, what's the problem with economy picking? Why are you changing?

Once I changed too but I didn't gained anything, but problems when changing strings. Nowadays I started to use the economy picking and now I can even skip a string. And there is no any audible changes, unless you don't use high gain distortions.