My group has always had a huge number of languages (no standard PHB languages, but rather regional and cultural), partly because of DM control and also to preserve the sense of the mysterious and foreign. We tend to have a regional Common that all players must speak, but it is by no means necessarily spoken world-wide or even culture-wide.
I like the notion of adding skills to the list rather than a trained skill slot, but this in particular seems to lend itself to abuse. When the Ranger multiclass feat is already somewhat optimal because of the access to Perception, it seems like a no-brainer if this were to be accessible through a decent Int. I would further condition this suggestion with a DM-written list of allowable skills to train, to preserve the skill system's class distinctions.