No ships = no blockade, and being weaker than you His Holiness takes their side, kinda like Daddy punishing you for punching your little brother after he kicks you in the crotch. Send a couple of assassins to visit the Pope and make him an offer he shouldn't refuse. That'll take care of the ex-comm.
In most of my campaigns, except this last one, I find the Byzantines to be one of the first with a navy, I always try to get allied with them at first, so they don't snuff out my trade. This time it's the Egyptians dominating the east, so I've held off on the Crusades in the eastern Med and am trading with them for now to build up a big enough war chest to survive the eventual loss of trade. The Mongols should be hitting the Egyptians around 1260, 20 years from now, I'll make my move then hehe. I prefer to play the glorious achievement game, the total world conquest I don't really like.
The diplomacy part of the game needs some work. Once your empire gets too big all the other factions gang up on you, and there's no alliances to be had with any of them. It seems the AI would rather fight to the last man last province instead of survive, which in the glorious achievement game should not be, because it turns into conquer the world instead. Better diplomatic AI would improve this game immensely.

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Diplomacy is the art of telling someone to go to hell so that they look forward to making the trip.