Initially, MDG announced that they would deprecate Blaze, but they changed their mind - more about that here. I’d try React if I were you, but Blaze is definitely staying viable.
I’m pretty sure it still works, but I’d definitely go for Flow-Router, which is really easy to use. You should also consider React-Router if you’re diving into React. Meteor has also put up an opinionated guide to developing apps with Meteor, which is absolutely great if you want to get going. It will be actively maintained to follow future releases.
I would like to know more about this problem with themes, you’re having. Can you maybe describe it in more detail, and perhaps share a simple example of what you mean?
It’s being implemented in browsers as we speak, so yeah - I think that would be the proactive thing to do there’s benefits to reap, and with Meteor’s upcoming 1.3 release (probably around the end of february/early march) we’ll have ES6 Modules (import/export).
Backwards compatability is the name of the game, so it shouldn’t!
There are at least a couple Meteor friendly templates, but in my experience it’s not to hard to convert a bootstrap theme. Start with a bootstrap package, and just work out the issues one by one. I start by turning off most of the third-party scripts and just enable them as needed.