> Thracian has been conclusively shown to represent a different branch of Indo-European than Albanian,
Has it?
And to the intonation thing, maybe I worded it wrong, as English is obviously not my primary language, but I'd say each and every language (or the great majority of them, anyway) have a distinct way of pronouncing their words. For example Italian, which I managed to learn just by watching TV as a kid, has definitely a different intonation compared to how we, Romanians, speak, even though they're both Romance languages and pretty close (closer than Romanian is to French, for example).
Close to us, I find that both Serbs and Bulgarians have different intonation compared to Romanian.