"I keep building ships but ending up disappointed by a couple of things. For example I really wish I could build the command towers myself, there are a ton of places for casemate guns I don't want or that I wish didn't exist and places I WISH I could put them, I cant."
It would be nice if we could get ability to seal casemates placements.
Also about building your own command tower... i don't think that is important, it would be nice but not exactly necessery, maybe when the game will starts heading out from Beta to Full version, then complicated things like that would be great addition to the game (yes, i'm saying this is complicated, because devs would need time to separate each important part of the command towers).
"I got this thinking I could lego together ships, Instead I get stuck with a Hull and I can extend or shorten it. That's it."
You can extend/shorten hull by adjusting displacement... and this is correct, because the bigger ship, the bigger displacement will be and same the other way.
"Hell, on the heavy cruiser hull, the super cool side turret rings I usually can't even effectively use because the only towers available for it get in the way of atleast one set of them"
You propably mean Italian Heavy Cruiser hull/superstructure, and even if not, the best solution to this is changing gun caliber and also rating the turret.
Example below, it works on every ship and superstructure.
"Most ships I build also end up being a tad bit of an eyesore."
True, very true.