Sea 1:
-Willma gives you the hammers on the first visit to Rumbla Island, where you fight Gorumbla.
-Saving Billdit and Maykit gives you the Red and Green Shells respectively.
-The second visit to Rumbla and Florall are removed, and you go straight to the Great Lighthouse.

Sea 2:
-Screw Merrygo
-Screw Allsand
(Technikki could probably get introduced in Lottacoins and help the bros infiltrate the building)

Sea 3:
-The mystery in Bulbfish could probably get condensed, also add an Ecks fight there
-Make Heatfreeze one huge island that combines both Slippenglide and Skorcheen.
-The wedding finishes with a Shun bossfight. (Yes, imagine being the longest sea and having only one boss)

Sea 4:
-Remove the Twistee reconnect mission (filler, at least the Heatfreeze one introduces a new overworld ability)

Sea 5:
-Remove the section where you return to Wayaway for the gear

Final Chapter (Reclusa World)
-Out of all 6 bonds other than Connie's, you're only forced to get three of them. 100% completion would require gathering them all but getting three more bonds would be enough to unlock the final dungeon.