if you cant econimy pick very well then the alternate method is better. i am not good at econimy picking, so i find it easier to alternate pick everythin. if u can econimy pick then do so. the only thing with econimy picking is it seems to taske planning to me. when i improvise i decide what note i want to play then play it. if i was econimy picking i would also have to concetrate on what my right hand is doin. where as if i strict econimy pick i dont. because its just up down up down. no decisions made. this makes it easier to improvise, for me.

it is always good to have good alternate picking to fall back on when econiy fails, at least thats my thought.

only other thing is i find i can keep rythm better with alternate picking. i dunno if this aplies to you.