I've finally found some time to download and read the original document, and the commments. So here are some of mine.
I found the updated speak language skill to fail the sniff test. The average (Int 10) native speaker only has a 50% comprehesion of another native speaker? I would hope that two native speakers could have a slighly higher mutual comprehension.
I liked the comment of instead of using a skill check for the speak languages skill, applying a penalty to other skills which use language based upon the relative lack of fluency in a language.
One point I've not seen addressed is that speak language is not just a one person activity, it requires two people; the speaker and the listener(s). And the level of comprehension depends upon both of their skill level. If I (who knows three words of Japanese), try and speak with someone who is fluent, they will have an easier time of understanding me than someone who is only partly fluent.
I would not ban Comprehend Languages as a spell. If they players are willing to accept the added complexity of the liguistic rules, I would make some modifications to the spell. The spell allows the players the crutch of a "common" language without there actually being one. It makes them dependent upon the spell caster and/or magic items. Or they can learn languages.
I would have Comprehend Written Language as a divination spell, and use a Detect Thought/Telepaty type spell to read peoples mind.
Generating Custom names:
http://www.ruf.rice.edu/~pound/
This page contains a whole list of name generators for various languages, items, and so on.
