I am not sure if this is the answer you are looking for or not. The question "East Indies oil" was arguably where the Pacific War started. But that's not where it ended. Why was that?" makes it sound like you are asking why by '45 was Japan still not investing resources in obtaining Dutch Indies oil, but it could also be interpreted as why did the USA and Allies not force a final battle in the southern theater as opposed to concentrating all its forces against Japan proper.
Also, a lot of the numbers that I have seen regarding the oil used and stored are not consistent among authors which makes drawing some conclusions difficult, but by '43 Japan was able to restore Dutch Indies oil to about 75% of its former production and was obtaining approximately 50 million barrels of oil, in fact in early '43 Japan did not really have a problem with oil, in fact they may have even had a surplus.
"Within a short period, Japan was able to restore the Balikpapan oilfields with astonishing results that far exceeded their goals. Oil production in the Southern zone in 1940 was 65.1 million barrels. In 1942, the Japanese managed to restore 25.9 million barrels, and in 1943, 49.6 million barrels (75% of the 1940 level). With the East Indies oil, Japan was able to import enough oil to make up for the oil embargo in July 1941 by the Americans, British, and Dutch. There was no lack of oil, and the Japanese fleet could even refuel locally at will. They even struck a giant field in central Sumatra in the Minas structure. All these events helped make Japan feel that the oil problem, which was the driving force for its aggression, had been solved." 
In very late '43 and into the start of '44 they started to experience oil problems again, to alleviate this they reduced civilian oil consumption to 4% of 1940 levels and started to explore other options like increasing synthetic oil production (which never amounted to more than a couple million barrels a year) and production of pine oil, castor oil, and even sake, but this again amounted to only about 1 million barrels per year and was never a real long term viable solution as it fouled their engines up and was extremely labor intensive. They were also still able to get small amounts of oil out of Manchuria but transport and logistics of doing this were immense.
By '44 they were again in a massive oil deficit, they could only partially fill their fleet for the Battle of the Leyte gulf.
"Eventually, the urgency of fuel led the Imperial Navy to throw all of its weight into the Battle of Leyte Gulf off the Philippines in Oct 1944 as the noose was then growing pretty tight. The shortage of fuel handicapped the Japanese again and again, and the 3-day battle led to a devastating defeat for the Japanese." 
The loss of all this shipping tonnage greatly reduced their previous requirements for oil simply because they had less ships to put fuel in and did not need as much oil as before and the ships they did put oil in were only partially filled because they were constrained to operating much closer to the home island. So by late '44 and '45 when they were pretty much out of oil they were stuck without options. Their meager production of synthetic oils, pine oil, castor oil, etc, were enough to mount some defensive operations but it was not enough to mount another campaign down south to secure their supply lines.
I would argue that the Battle of Leyte Gulf was Japan attempting to reopen lanes to the Dutch Indies, because once the Philippines were occupied and secured traffic and communication lines to the Indies would be effectively severed. After Leyte Japan did not have the ships (merchant and military), pilots, or manpower to operate in the southern theater aside from ships that already existed there and if those ships were pulled out and sent to Japan it was a one way trip.
"' Reno I ' was based on the premise that the Philippine Archipelago, lying directly athwart the main sea routes from Japan to the sources of her vital raw materials and oil in the Netherlands Indies, Malaya, and Indo-China, was the most important strategic objective in the Southwest Pacific Area. Whoever controlled the air and naval bases in the Philippine Islands logically controlled the main artery of supply to Japan's factories. If this artery were severed, Japan's resources would soon dry up, and her ability to maintain her war potential against the advancing Allies would deteriorate to the point where her main bases would become vulnerable to capture... Strategically the Halmahera-Philippines line had been penetrated and the enemy's conquests to the south imperiled by an imminent threat of Allied envelopment. The rolling up of the remainder of this line would cut off in the Netherlands East Indies the Japanese Sixteenth and Nineteenth Armies, a force estimated at nearly 200,000 men, and would sever essential supplies of oil and other war materials from the Japanese mainland" 
MacArthur said in his reports on 10/25/44:
"The strategic result of capturing the Philippines will be decisive. The enemy's so-called Greater East Asia Co-Prosperity Sphere will be cut in two. His conquered empire to the south comprising the Dutch East Indies, and the British possessions of Borneo, Malaya and Burma will be severed from Japan proper. The great flow of transportation and supply upon which Japan's vital war industry depends will be cut as will the counter supply of his forces to the south. A half million men will be cut off without hope of support and with ultimate destruction at the leisure of the Allies a certainty. In broad strategical conception the defensive line of the Japanese which extends along the coast of Asia from the Japan Islands through Formosa, the Philippines, the East Indies, to Singapore and Burma will be pierced in the center permitting an envelopment to the south and to the north. Either flank will be vulnerable and can be rolled up at will." 
Japanese Admiral Toyoda, in after war interrogations, said as much when he stated:
"Should we lose in the Philippines operations, even though the fleet should be left, the shipping lane to the south would be completely cut off so that the fleet, if it should come back to Japanese waters, could not obtain its fuel supply. If it should remain in southern waters, it could not receive supplies of ammunition and arms. There would be no sense in saving the fleet at the expense of the loss of the Philippines." 
By this point getting oil from the Dutch Indies was a moot point, unless the ship was pulling up and filling right from the field, they could not get the oil to where it was needed due to the US submarine campaign, control of the sea lanes, and lack of transport ships, specifically oilers. Japan could simply not build merchant ships, specifically oil tankers, as quick as the Americans and Allies were sinking theirs. Also with the capture of the Philippines their sea lanes to the Indies were severely restricted, mainly being running in shallow waters along the coast of China where US submarines had more difficulties operating.
"The real problem was getting the oil to Japan. The Japanese tanker fleet was never adequate, and insufficient priority was given to building more tankers. Hence much of the production from Southeast Asia never made it to Japan. Although production in Japanese-controlled areas peaked at almost four million barrels a month in 1943, imports to Japan never exceeded about 1.4 million barrels a month. In the last two years of the war, the Japanese Fleet lost its advantage of interior lines of communication because of the necessity of basing much of the fleet near its fuel sources, at Singapore or Tawi Tawi" 
So to answer why the war didnt finish in the Dutch Indies is because by then it had become impossible, in '45 Japan could barely sail out of their home waters, they had ships stranded at home because they were out of oil, so it was already too late in the game. Their overall war strategy had changed from being a war of establishing an empire and securing vital resources to being a war of survival, and they adjusted their plans accordingly. Realizing this they chose to concentrate their remaining forces in the places they did and attempt to make the US pay as much as possible for any ground they took in an attempt to increase their negotiating power. A further attack down south was completely out of the question.
And as Mark Olson mentioned below, the Americans had no desire or need to force a final battle in the Dutch Indies, the Dutch and British islands were already isolated and "withering on the vine." It would be foolish to waste manpower in the south when the Allies had decided the final battle would be in the north against Japan itself.