Alright I am definitely tying my hands a bit too much now.  The collection of non-negotiable requirements I placed on this build forced it into a fairly specific shape & layout that unfortunately could not look good.  Looking at it with the almighty hindsight I actually feel most of it was done right at a high level, with fine details always being debatable.  The problem was all in the constraints.  Without those constraints, though, I'd have a ship in official LEGO style, with the deck level area of the superstructure being 1/2 the height of a minifig, and absolutely no consideration for how figures could potentially get up to the bridge.  I have, in fact, begun to find some of the limits of what can be accomplished with LEGO, with consideration for minifigs, at a reasonable size.  Making everything much bigger would solve all of these issue, but also completely break New Jang City as I'd end up with only 4-6 buildings and 1 ship taking up the entire room! Things that make ya go "Hmm."

Video: New LEGO Cargo Ship MOC -- Break Bulk Carrier (not good)