I personally prefer starting in manila, then moving as the front lines change. Distances travelled are about the same as if I was out of Pearl, but there are more aircraft and warships to be encountered. There are also a couple of sweet spots where the islands form a beautiful funnel for merchant shipping. One thing about TMO is that speed is crucial for fuel consumption. S-Boats are fuel efficient around 7-9 kts, Porpoise, Salmon, Gar, and Narwhal seem to get the best around 10-12 kts. Weather is also a major factor as well as battery charging and sitting still, since the diesels are considered to be running. You will have to play around to find what works best for you.
Edit: Stay away from the Java sea unless you want a short career...