Using Boss Door Clipping and the Ocarina Glitch, it is possible to skip the Flippers, saving about 1:30 minutes in the Any% run. The only uses of the Flippers are to enter Temple of Droplets and obtaining a key to reach the lily pad. Detailed below are ways to skip both of these sections.
Since you don't have the Lantern when entering Temple of Droplets, you will first have to acquire the Magical Boomerang to perform Boss Door Clipping.
To obtain the Magical Boomerang, you have to do the four Tingle Brother fusions:
Tingle in South Hyrule Field, GP required (fuse AND talk to him afterwards to fully activate the quest)
Knuckle in Trilby Highlands, GE required
Ankle in Lon Lon Ranch, G> required
David Jr. in Lake Hylia, GP required
These fusions will open up the trees in North Hyrule Field, allowing you to open the chest and obtain the Magical Boomerang.
See the page for various manipulations for Kinstones in Any%
Since the entrance to Temple of Droplets can normally not be reached without the Flippers, you have to activate the Ocarina Glitch off of the house on the top-left side of Lake Hylia to walk over the water instead.
To open the door, you can either use Yadra's setup below, or Ezlo Buffer to a specific bomb frame.
In order to skip all rooms with water in Temple of Droplets, you can use Boss Door Clipping and the Ocarina Glitch to gain access to the Blue Warp Room Early.
After obtaining the Boss Key, save & quit and activate the Ocarina Glitch. Go back to the beginning of the dungeon and use the Magical Boomerang to clip past the Boss Door. In order to correctly clip upwards after triggering the screen transition on the right, you will need the correct subpixels:
After clipping past the Boss Door, roll to the right 3 times
Roll up against the wall and use the Cane of Pacci to check the subpixels (use the video and image for reference)
Should you not have the correct subpixels, walk down a tiny bit and repeat the action
Once the subpixels are correct, roll to the right and pause immediately after the screen transition to clip into the wall
Press Up or Down briefly to clip on top of the wall and then transition the screen left, up, right and jump down into the Blue Warp Room