The longshot can be skipped by crossing the gap leading to the door. There are multiple methods, but these are the most useful.
Initiate a Superslide then equip the Hover Boots. When you start to hover, let go of R and hold down to grab the edge.
Do four contortion hovers then backflip to cross the gap. Alternative hovering options include: sideflip hovers, slingshot hovers, hover boots hovers, angled backflip hovers.
Get on the middle platform and face the boss door ledge. Turn around and get against the wall. Strike the wall with the Megaton Hammer and then pause. You are looking for the frame where the point on the back of the hammer is right next to Link's head. Now equip the hover boots and unpause. Simply run forward and grab the ledge.
To do this you need to Bomb Hover using either bombchus or bombs until Link's head is in line with the wooden frame of the boss door. The easiest method is to place the initial bombs for the staircase hover with your Kokiri Boots on, before switching to the Hover Boots for the actual backflips, and then doing 3 bombchu height hovers. It is also possible, but harder, to start the staircase hover with the hover boots.
If using bombs, 3 bombs is optimal. If more than 3 are used, or if you gained too much distance with your hovers, a forwards sidehop (sidehop forwards out of a side roll) may be required. Otherwise, you will be too far away from the door when you jumpslash and will not clip through. One must jumpslash immediately after the sidehop and also hold forwards.
This can also be done using only bombchus, as shown below:
In the room where you can lower the water level to the first floor, there is a bombable wall on the second floor that contains a key. Normally you would have to raise the water to the second floor to reach it, but it can be reached by side-jumping into the corner, then using a jump attack to land on the ledge.
In the room with the spikes blocking your passage to the Boss Key, you can get past them without the longshot.
With a well timed backflip near the end of the hover you can land on top the spikes.
Hover along the wall to get past the spikes.
This requires the iron boots and the hookshot. Use the torch on the bottom floor to clip out of bounds then swim to under the platform that leads to the boss door. Swim off the edge and jumpslash to land on top of the spikes.
You can get into the doors on the second and third floor of the Water Temple without raising the water level. Perform a Hover Boost in the direction of one of the doors and right when the hover is about to end, you should be just in front of the door. If you look carefully in the video, you can see the A button very briefly reads "Open".
If you want to return to the top without savewarping but the water level is too low, you can use the pool of water at the dungeon entrance to float back up. Just torch clip to get out of bounds, then swim to the water at the entrance.
Beat Dodongo's Cavern without getting the bomb bag. Before you pull the Master Sword, go Bombchu Bowling and win the Big Bomb Bag. Now go back to Dodongo's Cavern as adult and obtain the Bomb Bag. This will put a Bomb Bag over your Bombchu slot.
Alternatively, you can also use DoT Skip to get around having to beat Dodongo's Cavern. You can then RBA Cojiro to modify your left side equipment with 2 bomb bags. Now simply open the bomb bag chest in Dodongo's Cavern as an adult to get the equipable bomb bag. Note: You must have a bomb bag in your inventory to get this equipable bomb bag; simply skipping the one in DC and going back to get it as an adult will not work.
Now go to the Water Temple with a Bottle on B and the Bomb Bag you now have on C-Right. Now if you empty or put an item in the B Bottle, you'll receive a number of Water Temple Small Keys equal to the hex value of your B Bottle. See Reverse Bottle Adventure for more information.