i dunno, i really find that when i'm economy picking, it's harder to get it rhythmical, whereas alternate picking runs,to me, feels comparitively very rhythmical... and while alternate picking may seem technically more difficult, it means that you dont have to think about when to do 2 upstrokes/downstrokes in a row.
but i definitely think its a good idea to have a grounding in both, no matter which you decide to choose in the end.