Another thing you can do is alternate which direction you begin picking a scale. For instance, most guys will start a scale with a downstroke and then alternate pick the rest of it.
Instead of doing that, start the scale with an upstroke and pick every note the opposite of what you'd normally do.
If you spend half of your time practicing in reverse like this until it becomes natural, you'll find yourself not even noticing anymore which direction you're picking in. That way you aren't always limiting yourself to starting leads on a downstroke for instance, or worrying about getting lost in the middle of a lead and having to suddenly reverse direction.
(hard to explain in words.. hope that makes sense)