Israel does not want to be in charge of those areas, and has already given most of the area to Palestinian sovereignty.
Before 1993, Israel was in control over the entirety of the West Bank and Gaza. This was a result of the Six Day War. To summarize, Egypt blockaded the Strait of Tiran, and surrounding Arab nations prepared to invade Israel. Israel preempted, destroying Egypt's air force, and drove the Arab nations back. This resulted in the capture of the West Bank, Gaza, the Sinai, and the Golan Heights.
There are around 4 million Palestinians in the West Bank and Gaza. Combined with the number of Arab Israelis, this puts the Arab population west of the Jordan River approximately equal to the Jewish population. Israel wants to remain a Jewish state, but cannot do so if it annexes the entirety of the West Bank and Gaza while remaining a democratic country. This is why Israel has offered Palestinians land equivalent to the entirety of the West Bank and Gaza a number of times.
However, the annexation of all territory in the West Bank and Gaza would not just be a demographic problem, it would also require the retaking of land already given to the Palestinians. In 1993, Israel and the PLO agreed to the Oslo Accords, which granted Palestinians around half of the land in the West Bank and Gaza. In 2005, Israel withdrew from Gaza. The Oslo Accords were only intended to define interim borders until a final settlement had been negotiated, but in the mean time, Israel recognizes Palestinian sovereignty over the areas specified in the Oslo Accords.
Israel does not want to capture all territory west of the Jordan River, nor should they. Even if it is militarily feasible, it would be a political and demographic disaster.