Yeah, I found that a bit weird as well, there is some logic in the manoeuvre as it puts all your valuable assets out of harms way (bridge, hanger, etc), and the idea was to lure the enemy in to the weakly defended belly so the bombers could make surprise attack runs, but I know what you mean. Another factor is how effective the bombers were against the capital ships, it took only one run to take out most of them. What did the droids do? Switch off their shields just because they were attacking the enemy vessels belly? It did seem a little too easy when compared to the first attack earlier in the episode where there are 3 Republic Destroyers vs a Seperatist Command Ship and 4 Frigates which results in the Republic forces retreating having lost one vessel with another heavily damaged. Then with the second assault, sure Anakin takes out the Command Ship and removes the Seperatist Commander from the picture, but these factors wouldn't logically lead to one surviving Destroyer being a match for 4 Frigates whether they have a Commander coordinating them or not.
Heh, despite these minor gripes I too enjoyed the episode a lot, too much in there to enjoy to nitpick too much.
