Meteor used to be black magic. They used to reinvent everything and this caused them all kinds of trouble. They even claimed NPM was a bad match for Meteor because "it's not isomorphic enough" (whatever that means when talking about a package manager). The most blatant problem this line of thinking caused was their hard dependency on MongoDB and an increasingly outdated and exotic front-end framework that didn't even provide server-side rendering capabilities.
However things have changed. Meteor has replaced its front-end components with React and the database communication is being replaced with Apollo (i.e. GraphQL). They're even embracing NPM now. This is a good thing.
The only fly in the ointment is that now that all the major components have been replaced there just isn't much left that gives Meteor the edge over other stacks. It's just an opinionated React stack with a few weird idiosyncrasies that don't provide any obvious benefits. It hasn't become any worse, it just has become obsolete.
Meteor had a good value proposition when the main competitor was AngularJS 1 and the majority of new websites were still being built with Backbone. Its target audience were beginners who weren't yet invested into standard JS tooling (i.e. NPM). That value proposition no longer holds up today.
So in other words: Meteor has tried to shed a lot of its magic but the magic was only part of the problem. The real problem is that it tried to be a huge monolithic solution that was completely incompatible with the existing ecosystem. That has changed, but it is just too late. Parts of it may live on (e.g. Apollo seems to be getting some interest if not adoption) but as a whole it's simply outlived its usefulness.