In other words, is it possible to delay the story progression (and therefore tougher enemies) through not researching certain artifacts and not doing certain missions? Is it possible to "fail" story missions or suffer other consequences by not doing them for prolonged time?
From what I've been finding, the story mode is all unlock based. You have to research certain items or go to certain places for the story to unfold. However, this does not stop bigger and badder enemies from coming out at you. There are a few story-based enemies that come out, such as the Outsider or the Sectoid Commander. But I found that by delaying the main story and just playing the game, you get harder enemies, whether you like it or not. For example, I had to build a certain thing in game, but have put it off for a few months. As the months went by, I started to get harder things, like Cyberdisks and Berserkers. I'm sure if I keep this up, I'll find new and interesting aliens as well.