Definitely. I kinda know how Meteor works and how it achieves its reactivity, but it's still too much of a black box. It's really frustrating, because this disables you to perform optimisations. I recently stopped working with Meteor, because it feels like it's really bloated and the reactivity seems very unnecessary at times (despite really loving the developer experience).
When I started writing raw Node applications it felt really good to have control over nearly everything. The problem with Node stacks these days though is that you have to spend an enormous amount of time on configuration. That's where boilerplates like MERN come into play.
In the end it all comes down to your application requirements. Meteor makes it ridiculously easy to build realtime applications, but feels quite heavy and it's too much of a black box. For now, I'd go with the Node stack, as long as you use a boilerplate.