Goten still lived with him for years the Buu saga so it's not like they where estranged!

Actually the one prior to Gen 1 was only implied. It's not explicitely stated that a war took place in KANTO, but it took place recently enough that Lt. Surge had fought in it (and presumably earned a medical discharge as he looks a little young to be retired).

In the games only one other war was explicitly confirmed to have happened, which was the Kalos War, 3000 years prior to Gen 6, but several smaller scale conflicts have been implied to have happened at various points the legend of the Veilstone Sword being one of them , and it could be argued that fighting between Team Magma and Team Aqua and even Team Rocket's more bold operations in Gens 1 and 2 could be considered small scale wars in their own right if we think about their probable impact in realistic terms, as in both cases they were apparently capable of effortlessly overwhelming local law enforcement and possibly military forces to the point of total impotence, otherwise the police would've been defending the Silph Co. or Radio Tower from Team Rocket. .