What were the MAIN differences in the war in the Pacific to the war in Europe?By this I mean... Was their command structure different? What about...

There were differences in command structure for sure.  In
Europe, the US and the British had to share command with, for example, Eisenhower and
Montgomery disagreeing with one another quite regularly.  By contrast, the Pacific was
completely an American show.  There was no real need to coordinate with Allies in that
theater.

Another major difference was the sort of weapons
that could be brought to bear.  The European theater was influenced strongly by tank
warfare on the plains of Europe.  By contrast, the Pacific theater offerred very little
in the way of open spaces.  Fighting in the Pacific was much more reliant on infantry
and was done in jungle to a large extent.

In addition, the
enemy was very different.  The Germans were much more of a traditional enemy who would
do things like surrendering.  By contrast, the Japanese defended so unrelentingly that
very few Japanese defenders survived battles like those on Saipan and Iwo Jima.  This
made for a very different fighting experience.