In FF2/S, the sea flow goes from left to right, which makes sense with what you say, but Ilu is right about the bglayers/fglayers, try making them separated from each other and give them different speeds, that would help the stage A LOT on its look. Also, maybe the sea layer that is close to the raft should move a little faster so it looks more like rapids instead of a calm river, the current should be strong enough to move the raft after all.
The background character can also get a faster idle animation to 'ignore' the lack of animation frames, check how he looks in the original game, plus being at his spot on the background indicates strong winds, it would look better, same for the flags, making them move faster indicates strong winds, ask
@DCurrent about rapids environment, dude is an expert lol
You can also give the raft some 'rock' values so it moves a little up 'n down to resemble a boat behaviour.
After years of exp with the engine, just a few years ago I learned to pay attention to the stages as much as the playable characters and enemies, trust me, everything feels better when stages look as gorgeous and alive as much as they can.
Spawning some animals passing by would also make the stage look richer and more alive overall, make a few fish and some random birds

So far so good, looks like a good start. Animations need polishment here and there but seem very good with the given assets.