The only issue with Autothrusters is it's cost. 2 points is probably too inexpensive. Any upgrade that becomes too easy to spend the points on is not costed correctly. Spending your points should be a series of difficult decisions. AutoThrusters are worth more than a shield upgrade (even when facing non turrets). A shield upgrade is 4 points and Autothrusters is only 2 points. We should need to consider taking a shield upgrade over an Autothruster upgrade, but we never will simply due to it's cost. If Autothrusters was a 7 point upgrade, it would still be completely worth it, but many of us would seriously consider a shield upgrade instead of the Autothruster upgrade due to it's cost.
When upgrade decisions are too easy it creates a bad situation.