Common tongue doesn't really destroy the usefulness of Speak Language.
Speaking the native language, or at least being fluent will allow one a great deal of diplomatic/situational boost.
Speak Language is typically not too useful in campaigns where political intrigue doesn't take a forefront however (in my opinion).
Introduce necessities for learning languages besides the common tongue. Elementals only understand their elemental tongue, not common, etc.
Comprehend Languages is useful one-way (understanding), tongues is useful both ways (Speaking and understanding). Those are troubling issues, although they can also be addressed in a fairly simple manner. Consider the use of magical aides tantamount to having a translator walk around with you everywhere. It gets the message across, although you may miss out on specific inflections due to 'common' not having 78 different words for snow. It may also been seen as a bit insulting (or at the least, frustrating). For my campaign, well, it honestly hasn't really come up, except for my Cheese Gate Measure. 'Elder' languages cannot be translated by those magics. Sure, it's heavy handed, but it works to maintain some of their mystery.
Speak Language may typically be the most underutilized skill in D&D campaigns however

. Nothing quite wrong with it, and it sorta echoes a sentiment of not bothering to learn many languages once past their 'upbringing' period (ie, pre-adventuring).