Since the Caedeus quest is a repel quest his health is retained between quests. When I start a quest with him already wounded he starts in Area 3, forcing me to swim all the way there. It's both annoying and time consuming (~4 minutes). Are there any shortcuts in the ruins I can take to reduce the swim time?
Indeed there is! As with most maps, there is a shortcut from the base camp.
Looking at the tent, start on the left side, and run along the island's edge. You will very quickly jump into the water. This will spawn you in Area 2, approximately in the middle of the round area. There's still lots of swimming involved, but that should cut it down drastically.
If you really want to minimize your swimming time, the following skills will help with that, by reducing stamina drain, and increasing swimming speed: