Meteor's problems were rooted in its real-time protocol, DDP, which had some problems. Firstly, everything is real-time by default. It's better to minimize the amount of real-time components in your application as there are very few things that need to be real-time. Secondly, the pub-sub caching mechanism made it infeasible for situations with many concurrent users. I was able to get around this by proxying some of their internal functions.
Significant people in the ecosystem started leaving (e.g. Arunoda), probably for the same reasons. AFAIK, it's still the best JavaScript framework out there for prototyping and MVPs. Their accounts system makes whipping up a user-driven application trivial. MDG (the phenomenal team behind Meteor) is likely focusing their efforts on Apollo now, because they understand DDP's shortcomings. If you're interested in Meteor, I suggest looking into Apollo.