Ships are clipping on each other a lot since the last patch and small ones dont know how to go around bigger ships. Its ok to have them clip if they know how to go around, but until they learn it might be better to turn off clipping for ships within your own fleet.
Because you can no longer stack units on the deployment setup I think the clipping of ships should be reduced. Right now it really looks like ships are tripping over each other, and is a bit awkward.
Its possible to use this clipping as an advantage by putting smaller frigates behind a line of cruisers. This will keep the frigates slightly behind the cruisers until its time for battle. During the battle, the enemy will attack the closest target which is (preferably) a heavily armored cruiser while the frigates can just sit behind the cruisers and fire away. If clipping was off, it would go back to normal with the frigates approaching the enemy first and getting the front line of fire instead of letting cruisers tank for them.