I've thought about it a few times, but nothing that has really left me wondering. What I think is most likely would be if the dad was out on his own journey, since that's apparently the same thing with Ash from the anime's dad, and even Norman from Hoenn has been on his own journey before he settled down as a gym leader. So I guess it's just a common theme all over the Pokemon franchise.
As for your theory, Nintendork, it could very well be true, but I don't think it's very likely. The only person that ever mentions the war throughout the whole game is Lt. Surge, and he is a lieutenant after all, so it could've been another place than Kanto, although then again, it could be that most people just wanted to forget the war. I don't really think it's too dark for the first generation games, considering how many dark concepts and theories that are, just based around that region.