Hey!
That's a pretty impressive game project! I really like the Amiga/Atari aesthetics, and the flooding is impressive!
TLDR: my biggest mistake was picking squares over hexes. I would recommended hexagonal lattice even for real-time strategies. Unfortunately Blizzard doesn't feel enough competition to fix their competitive games and make the next Stracraft into a perfect game.
I am working on another pretty different XCOM inspired fantasy game, and I decided to go with hexes for the same reasons you recommended them, more or less.
What triggered me the most with squares was that formations don't work if both sides are not facing each other from the main directions, which should happen a lot in a game with large maps and fog of war (because you cannot have proper Zones of controls with squares).
However, it has been a huge pain to make walls and buildings, so I am still really torn about the issue. It really makes the wall tiles hard to read in term of blocking movement and LoS.
The NW->SE walls don't follow the hexagonal lines which causes all sort of issues.
I should have gone with natural caves instead of constructed walls.
So I am not sure you really were wrong about picking squares.