There is way to introduce aliens in the lore without breaking the main point of the franchise. if human nature will inherently lead to devastation, why wouldn't a more advanced species be able to exploit that? From what we know, the aliens are curious, if they were certain humans would destroy each other and wanted to test their hypothesis, they could have given it a "push".
But, it's subjective, people don't liking aliens in the Fallouit franchise as a whole is a subjective theme, some people will like, others won't. IMO, specially as an aspiring writer, plot can be interpreted into many distinct variations, there's no "correct answer".
Also, let's not forget, that there's also a chance Vault-Tec was responsible for the war, or at least, had a finger on it, following your logic, that would also undermine the whole "War never changes" concept, since, in the end, it wasn't human nature, but rather, the promisse of profit and the chance to run unethical experiments unhinged. The Enclave had a plan B which consisted in leaving Earth behind and collonizing another planet, Mars if I'm not mistaken, how to you think they got the technology necessary to allow for interplanetary travel? We know they knew about Aliens before the war, we have Skynet after all. In FO2, we also get the impression the crashed UFO was under military custody before it got "recovered" and dropped in the middle of the desert. You may not like it, but, at this point, we can no longer ignore the implications and call Aliens in Fallout a "gag", they're clearly part of the lore, whether we want or not, like T-60 Power Armor and fusion cores, I don't like it, but its part of the Lore now.