1) It's hard to judge how popular Meteor actually is (although as @awatson1978 pointed out, it seems to be popular enough on github). One of Meteor's sweet spots is custom apps, and those aren't necessarily seen outside the organization. We've moved most of our custom app development to Meteor from PHP, but none of that is public.
2) I have nothing to base this on, but I expect we'll start to see more Meteor stuff coming out soon. Meteor 1.3 is just over a year old, and I think for many that was a watershed release, with moves to get closer to the general NPM ecosystem. With time for people to start twigging on this and experimenting a bit, deciding to use it for the next project, dev time...I wouldn't be surprised if we started to see more Meteor projects hitting release soon.
3) MongoDB isn't appropriate for all projects, so being tied to it means that you're already limited to a subset. Apollo should make a big difference.
4) There has been quite a bit of churn. It's to be expected in new projects (and Meteor is still relatively young. 1.0 was...about 2 1/2 years ago?) If we had anticipated some of the changes between 1.0 and 1.3, we probably would have held off moving so much of our development until things settled down. I don't regret the decision, but when you have to deliver to a schedule and budget, you need stability. As things settle, I think we'll see more people jumping on it.
5) There are still pain points around deployment. Build tools were one reason why we went with Meteor over Node + Express + whatever. Moving from PHP, the node world is a very different beast, and ease of set up and building were more than welcome. Deployment, not so much, and not everyone who is experimenting is going to set up on Galaxy. More likely they'll grab a DO droplet and take it for a test drive. If that has too many bumps for someone entirely new to node apps, they'll try out the next shiny thing instead. (Even just good entry level documentation would be a boon.)
TLDR; there are a few actual drawbacks, but Meteor is young and I think we'll see more growth. Expect that there's a fair bit of behind-closed-doors projects in it.