If you think about it, there are two reasons air will "pocket":
- when the system is off, bubbles that aren't adhered to something with surface tension will tend to rise to a higher point.
- when the system is on, bubbles that are being carried along in the flow (entrainment) may stop being carried along if the flow slows down below some critical speed.
Beats me what you can do about the first problem, other than have a pump that's got enough flow to drag those bubbles back into the water stream when it re-starts - or to make sure all bubbles are gone before you shut things down.
The second one might be a non-problem if, even in the largest cross-section area the flow's still above that critical point (which I don't know) - or if you had a reservoir that slowed the flow enough that bubbles should come out
there. Maybe the thing to do, if you're not already planning to use a reservoir, is to try it without and see if you've got a problem - and add one if you do.
Just "thinking it through", feel free to tell me I'm wrong (although a "why" would be appreciated).