Why The war Isnt over

What the oracle said was true it just that Neo didnt go to the sorce pick 27 people to rebuild the matrix and have his code re-whateverd

I dont know if thats true though just a guess

But whatever has a begging has an End.

An instant seemed to be what would of happend. maybe a hibernation

a few years of Matrixcycle-time is quite right a blip, but the age of mankind (5 million years) compared to the age of the universe (13.8 billion years) is also a blip. but in that short timeperiod a lot can happen. Although it's relatively small, to us it can be a long period in which much time can pass and a lot can happen.