Is it kind of stupid and pointless? Sure. But I hardly see how it's something worth getting this pissed off over. It'll probably be a short sequence in the game, not something that's forced upon you throughout the entire thing.
This. I mean past AC games had you using a winged flying machine that would get massive increases in altitude by small fires. They are simply taking a fairly slow paced and probably fairly mundane concept and making it more video gamey. I mean if you want realistic naval battle, might as well play a strategy game and not an action-adventure game centred on platforming and close quarter combat.