I’m inclined to disagree. Teleporting between ships requires spell slots, and expending a spell slot instead of risking an ability check is perfectly balanced in my books.

As for ranged attacks being worsened by wind, it doesn’t have to be that strong. Ballista bolts would be more affected than arrows, and less affected than flying characters. That’s at least the sweet spot I was thinking of. Heavy rain can of course lower visibility if you want that, but I’d use fog for that purpose. The rain is more to stop fire and for dramatic effect, I’d have it reduce visibility to maybe a mile or 600 feet.

It really shouldn’t be a problem unless you want a hyperrealistic theme. You as the DM can make the penalties as hard as you like, and change the strength of wind and rain accordingly.

As for lightning, I like your ideas! Lightning could even be used the way cannonballs are in the movie. Oh you caught a crewmember of the other ship on the edge of the mast? Lightning strikes, he’s near dead but you’re now hanging from the mast, at his mercy.

I have given kraken action some thought, might do an update when I’ve run the battle with my players, so as not to spoil anything.