I would go with the first dot gives one language, the second dot gives two more, the third dot gives three more, and so on, for a total of 15 languages at the end. Though there is a person that knows 27 languages, since he travels the entire world buying stuff to sell in those nifty little "Third Planet" stores, so maybe the total should be larger.

I like the concept, as the language rules are unpleasantly grainy.
I'm not so sure I like how it handles characters who know a smattering of many languages. The fact that fluency in all known languages is set by Linguistics score means no PC ever gets an excuse to drop a line like, "So... How's your Flametongue?" "Uh... a little rusty."

Also, the significance of "fluency" isn't defined at all. I can only guess that fluency is the number used for Linguistics rolls for that language, but I'm not sure.

A few possible suggestions:

Each point of Linguistics gives X number (say, Intelligence) of fluency points, which can be distributed among any number of languages.

Or, each level of Linguist gives Linguistics fluency points per level.

As for fluency, I might handle it in terms of vocabulary. Any given document or speech would have a Vocab (or something) rating that indicated how complex and specialized the diction is. 1 is a children's book, 2 is a pamphlet made for the masses, 3 a typical novel, 4 a technical manual, and 5 being the most obscure, archaic language.
Then, apply a penalty to any Linguistics roll when the PCs relevant fluency is less than the vocab rating of the text/speech.

Additionally, you can use Vocab as a limiting factor of the effective Linguistics of a written social attack. The more eloquent your prose, after all, the more literate your reader needs to be.

In any event, the article was good food for thought.

Hmm. I think the original rules are workable. I don't like to try and fix things unless I really have to. I think Linguistics is good if you look at it right. The dots represent total fluency. You can make an Intelligence+Linguistics roll to make a statement in another language. This means that if your total dice pool is 7, you get 1 free success at all times. You are sufficiently schooled in languages that you can ask where the bathroom is anywhere in Creation.
Also, as a Storyteller, I would allow a character who had reached a dice pool of 7 or higher to swap out one language for a new one, if it made sense. If you had spent a long time in the south, you could pick up flametongue, but at the cost of losing Icetongue or Low Realm, if your character hasn't spoken them extensively in a decade or two. You could still use the Linguistics autosuccess, but you could honestly claim to be "rusty" in that language.
This obviously isn't something that you could do on a regular basis. Only when it really makes sense.

We have dealt with the same issue in our games as well. We handle it by simply squaring the dots you have in the ability. These points are then allocated in fluency and literacy. So you can speak a load of languages and read some, or be completely fluent in just a few. Though these rules work just fine too :D