They want Instagram to be mobile only. Instagram was always mobile only until recently they added some desktop functionality. It would make sense that they really want to differentiate Facebook from Instagram. They may do messaging on desktop in the future, but it's probably not likely.
From a marketing standpoint, impressions on mobile exceed impressions on desktop. Since they already have Facebook optimized for desktop, Facebook captures market share of ad spend on desktop. Instagram, optimized for mobile, captures market share of ad spend on mobile (this statement isn't 100% true because Facebook mobile captures significant ad spend, however the experience and demographic is different on Facebook mobile vs Instagram mobile).
In terms of maximizing business revenue (also user experience), a company would want to cater to their specialized audience. A generalized app or experience is not effective at making users satisfied. So Facebook as a company has a ton of demographics that they want to satisfy. They have many products: Instagram, WhatsApp, Oculus VR, FriendFeed, LiveRail, and 80+ others (https://en.wikipedia.org/wiki/List_of_mergers_and_acquisitions_by_Facebook).
Back in the days of MySpace, user experience was highly customizable. MySpace users can fully edit their profiles. Falling letters were the rage, changing colors, divs, widgets; and a lot of users in MySpace generation learned basic HTML/CSS/coding (interestingly enough, a lot of these people are now in tech roles, creating products like Facebook, Uber, Instagram).
Nowadays, less is more. Companies need to be at the forefront and decide what users want, before users know they want it. Less features, less functionality, and a simple, intuitive user experience are what the people want.