Spend enough time in the classics and biblical languages mini-spheres of the internet, and you will encounter various wars that have been going on forever, but high-speed internet has globalised them and speed up their delivery systems. Pronunciation is one of those.
It's less of an issue in the Latin orientated communities. Restored Classical pronunciation is fairly well established, at least as an academic norm, even if it's not always well practised. People recognise Ecclesiastical pronunciation for what it is, and why it is, and accept it as such. The importance of recognising and utilising vowel lengths in spoken or recited language is also on the rise.
Greek, however, remains a minefield. There are at least 4 major systems in use, including Restored Classical (which few do well, since it involves tonal stress), Erasmian (widespread if only for its previous hegemony and practical ease), Restored Koine (see below), and Modern (used by those convinced of its practicality, and often uninterested in historical reconstructions). Then, I'd say, there are several botched attempts at the above.
My problem goes like this: I was taught on Erasmian, tried to shift to Restored Classical, and maybe got halfway. That is, I don't think I've quite got it, but I'm relatively committed to getting it right. Further, this has become fairly ingrained - I can read Greek relatively straightforwardly and aloud in this pronunciation.
I am, however, largely convinced that Buth, inter alios, is right about Hellenistic/Imperial Koine. This raises a number of problems for me. 1) I tend to read both Classical and post-Classical materials, dual pronunciation systems are likely to cause me additional stress. 2) The ingrained nature of my current position makes re-orienting pronunciation difficult. 3) I tend to read beyond the 4th century generally-proposed terminus for Buth's pronunciation as well - what then? Should I investigate Byzantine pronunciation as well?
In general, my advice to beginners is this: pick a pronunciation and stick with it. If you've got a teacher, go with theirs. Not sure what I'm going to do, but thought I'd share my thoughts.