Well,
Depending on the visa office, they probably have hundreds, if not thouhsands of applicants to get through...
and on top of that, I think the wait is partially to weed out those couples who aren't actually serious. If a couple is in a marriage of convenience and made the PR papers on a whim to see if it worked, they might lose hope after a few months and stop their communication, etc... but those who are in love and dedicated to a life together will wait through however many months it takes to live where they want to together.
But mainly, they have a lot of documents to verify, and have to judge if a relationship is genuine based on a few questions and a few pictures... Even with all of this verification there are still many people who get through the immigration process using fraud, which in turn makes it a more trying and grueling process for the real couples who just want to make a life with each other.
Some VO wait times seem like a walk in the park with their 3-6 month timelines compared to others which are 12-18 months. It all depends which country is seen as more desirable and generally has more to offer (more highly educated citizens, etc...) Doesn't always seem fair, but that's the way it is. Some countries are more desirable than others.... Some countries have more of a history of fraudulent applicants (marriage of convenience, fraudulent identities, etc) and so, like I said before, applicants after that are made to pay for other peoples' transgresions.