After thinking about it a little, there are some stages I'd like to see change a bit:
Arowana Mall: Maybe make the Splat Zones version the standard one.
Blackbelly Skatepark: Just for Rainmaker. Do something to prevent extremely fast wins, seriously I've seen games end near the 30-second mark, that shouldn't happen. Otherwise, I'm alright with this map.
Saltspray Rig: Make a way to reach the top area from each team's spawn-platform, maybe just extend the long part with a couple of walled protrusions onto that part of the stage. Might have to change the crane's path a bit to prevent hopping up into that part, but that can probably be done. Also after doing this, put the Rainmaker there, it'd make extremely quick victories less common and not as quick.
Urchin Underpa- oh right, they did that already.
Walleye Warehouse: Not because I have a problem with it, I just remember how it looked in the initial trailer. Specifically, the moving boxes in the center. Maybe put those in on one of the modes? Not necessary, I think Walleye is alright as is, I'd just like to see it somewhere.
Port Mackerel: I really dislike this map, it's just too many tight spaces for me. Maybe if they just had two rows of boxes in the center and one row in the corridors in front of each spawn point, or some way to climb up onto the boxes outside of Turf War. Or maybe just blow up the middle. I saw a pic with that idea, and I kinda like it (might just be me being salty tho).
Kelp Dome: I like this one as it is.
Bluefin Depot: Just for Splat Zones. Use the Rainmaker version of the map (maybe remove the bridge connecting the platforms and keep the ramps) and have both center rectangle platforms have a Zone. Not strictly necessary, but I feel like it would be better than the current one.
Moray Towers: Maybe make the Splat Zones version the standard one, I prefer that one most.
Camp Triggerfish: I'm okay with this one as is.
Flounder Heights: Too soon to tell on this one.