Is there any fear about overwriting too much of the base meteor functionality with some packages?
Example: Collection2 - In the future, if the vanilla Meteor collections change, will this break your app? That might not be a big deal. But, if you are so heavily invested in using Collection 2, it might be painful to update/remove all of that code. Maybe the developers of Collection2 will address that. If you do continuous integration, you might not catch the problem until its been deployed to production.
BTW, I use pretty much everything mentioned except Collection2. I just haven’t heard of it until now.