you shouldnt pick so hard as to lose control of when your pick is actually hitting the fretted note. One bad habbit is hitting the string with your picking hand before the note is fretted, causing a flutter effect on all of your runs. always remember to pick the note after it is fretted, not before.
Once you get your mind/mentally noted to the above, work in patterns of strict alternate picking, down, up down, down up down, down up down up, etc. do this vertically up and down the neck lightly and slowly, in each key, and in each register both low and high.
once you've gotten this down, work on picking faster using the above to help count starting out accenting the start. ONE, ONE two, ONE two three, One two three ONE, ONE two three ONE two, etc.
you can do patterns of 4 instead of three if it helps any - all depends on your personal preference.
work slowly to build speed - do not try to increase it too quickly, and only do so when you no longer need to think about the picking hand mentally and it becomes natural at that particular speed.
the faster you begin to pick the more control you are going to need. You shouldnt need to tense up, but you should not be so loose that you lose control and get sloppy. building this with the pyramid setup with licks you already know will help you out in the long run.
Personally i am a legato player at really fast runs, and if they need more normally i skip straight to tapping them out if i need to get to a note in a hurry. or i will simply skip strings or play part of an arpaggiated sequence instead. i never really liked strict alternate picking as i am more of a relaxed player. all depends on how you want to say what you're trying to get across on the fretboard.
