As written, the Linguist feat seems to be a poor choice for most players in most campaigns.
If languages are useful in your campaign, then the feat will be desirable. Making languages useful is difficult. If you make language use essential, then you run the risk of frustrating players when they cannot communicate with NPCs. "Hand signal" role-play is only fun the first time.
Don't make languages annoying
You want to emphasis complexity in culture, but you don't want to annoy players.
Hand-wave the common spoken languages. Just let characters talk to each other. Which languages are common depends on your setting. Probably the major races all speak a smattering of each other's languages. Another way to think of this: the old "Common" language is really a mash-up of useful human, elven, and dwarven words and grammar.
A little carrot: Make knowing languages useful
Emphasize the importance of being able to read exotic languages like Draconian and Infernal. Ancient books full of writing in these languages contain long forgotten secrets!
If a character "knows" a language, explain linguistic quirks to the player. For example, don't just tell them that the elf is angry; explain that the idiom the elf is using goes something like "I wouldn't waste a second on you," and because elves live hundreds of years, this is much more meaningful than if a human said it.
To give the Linguist feat a bit more bite, house rule it so that the player also gets a +1 linguist bonus to Diplomacy checks when speaking to a person in their native tongue and a +1 linguist bonus to History checks when recalling information about that culture. The bonuses apply to all languages that the character knows, not just the three new ones.
A little stick: Make not knowing languages inconvenient
Maybe characters know enough language to have a basic conversation, but their lack of true understanding hurts them when nuance of dialect is important. A character who makes a skill check that relies upon verbal communication, but who does not know the language, takes a -5 -5 penalty on those skill checks. Maybe even on checks involving nonverbal communication, since so much depends on culture.