Since I'm trained as a new linguist, not the old school you're referring to, I feel compelled to reply in order to correct some potential misunderstandings here. Structurally, you could also just take the position of Pollard & Sage (1994), for which they were so heavily criticized, and assume that every language on earth has the deep structure of English. By purely structural criteria many languages that historically unrelated would be somehow closely related to each other.
That is clearly not adequate if you want to take a look at languages and culture (in that language). Classifications of languages as languages are partly political, sometimes even highly political, and mutual comprehensibility is not a working criterion.
I don't recall the details, but the classification used by ethnologue.com are a fairly reasonable set of soft criteria. The alternative would be not to speak of languages and dialects at all, and instead only about varieties of various language families with a certain degree of mutual comprehensibility to other varieties, but that would be even more counter-intuitive to laymen.
As to your personal experience: That's sad, you merely seem to have ended up in the wrong department / with the wrong professors. Find some general linguists and computational linguists and you should get your global insights. Phonology was actually at the forefront of general structural descriptions, sometimes even earlier than in syntax. For example, they invented optimality theory. It's worth giving it another try!