I personally love the Captain of the Aquila costume even though I don't have it (sad story) To me the Captain Kidd costume seems too... gritty? I dunno, but I'm not too big a fan. --- I came here to chew bubblegum and kick ass, and I'm all out of bubblegum.
The CotA outfit looks absolutely terrible(I assume you mean this Captain of the Aquila outfit: http://images.wikia.com/assassinscreed/images/5/53/Captain_Aquila_Render.png )
If you're talking about the other Captain outfit...well I still stand by my love for the Kidd outfit but the actual captain outfit looks cool. --- "A man's dreams are an index to his greatness."-Zadok Rabinwitz PSN: THE_JOKE_KING33
The actual costume you wear when you're captaining the Aquila is the best one in the game. No idea why you can't just wear that one if you want... there are even some regular missions with it, so it's not like it's not a functional skin.
I like the captain of the Aquila outfit more due to the fact that it blends in with the other Patriots/blue coats better than the other outfits. That Kidd outfit reminds me of a funky Cossack getup. --- "Ignorance is thy companion!"