In my last campaign, I removed the comprehend languages and tongues spells specifically because I didn't want the mystery of languages to be overcome by magical means.
When my players magically ported to a much older continent with a different elven population, I used sylvan as their base language, and allowed those with elven to speak in simple phrases until they spent some time with the locals.
I don't try to make it too serious an issue. But it is important to use language to show that a place or thing is much older than contemporary times, and with it, comes some form of mystery and power. Otherwise, everything would be in Common. Boooooo-ring!