http://paizo.com/paizo/blog/v5748dyo5lc1y

This was written by the Lead Designer for Pathfinder.

"Gaining a language does not necessarily grant the ability to speak. Most animals do not possess the correct anatomy for speech. While a very intelligent dolphin might be taught to understand Common, there's no way for him speak it. There is also the issue of learning the language. The rules are mostly silent on this front, due to ease of play for PCs, but a GM should feel safe in assuming that it might take years to actually teach Common to an intelligent animal. All of this, of course, assumes that the animal even bothers to fill that language slot. Possessing the ability to use a language does not necessarily mean that such an ability is utilized."

The big takeways:

1) Animals cannot speak b/c they do not have the correct vocal anatomy.
2) At Int 3, the animal can understand speech the way a very stupid human can.  This is why handle animal is still needed for intelligent animals.
3) The rules don't say how long it takes an animal to become fluent in a language.  This one is open for DM interpretation.

Just my 2cp on the issue.

I just have to ask, what factors into vocal anatomy for this? A creature given intelligence, I would think, could learn to use its own vocal anatomy to replicate a language. While it might still be heavily accented, I would argue that its possible. Otherwise, how could creatures like Tengu (who have beaks) or any of the other more bestial races speak intelligible common?

Vocal anatomy is chord, tongue, lips ( I assume. Not mentioned here).

While a tengu (average INT 10) might be able to inatley speak common (all be it with some difficulty), a hawk with INT 3 is super stupid by human standards, and might not be able to figure it out.  I think understanding the language is one thing.  Thats why there are about 7 or 8 druid spells around communication with plants and animals.

I personally like the system where you have to make a handle animal check to still communicate and impress your will on a pet.  Then again, some people want to debate with Neil Degrasse Tyranosaurus over the finer points of stars in the heavens and what that means...

HAving seen the Rule as Intended (RAI provided by Pathfinder Lead Designer), do we, as a group, want to disregard that?

I am torn

I like the idea of having an int of 3 meaning something. If it takes handle animal either way, then what is the point in sinking an ability score increase into int, when str/dex/con are more combat oriented? I personally liked the idea of your bond having grown so much that you can talk to your animal and it responds.

I personally have never liked handle animal with your animal companion. This is a mystical bond between you and a creature who has chosen to be by your side, someone(thing) who(that) trusts you to guide it. I dont understand why I should have to try to convince it to attack. I have to make a check to ask my friend to lie down? To give me a hug?

Im sorry, im deviating from the point. 

I guess for more of a concrete response to your post, at what point does a creature gain the ability to think and understand a command? If I say to a int 3 human cohort* "punch him", does he understand what i said? how about my int 3 animal colort*? Is the handle animal required because of it's inteligence, or because its an animal? if i boost said animal's intelligence to 13 through means other than awaken, do i still need to make handle animal checks?

While I understand (partially) what this game creator/designer/writer guy is trying to say, where do you draw the line? To me, the line was drawn at "It gains a language" when, while i agree it cant speak it, it understands what you are saying (for the most part)

* I'm using the term cohort as a trusted companion, whether it be due to leadership or to paladin mount or animal companion, etc.

So there are two points here.

1) When does an animal understand what you are saying?

-An animal always has the ability to understand somewhat what you are saying.  An int 2 dog (thinking of Badger and Lola) can get the gist of a command based on teh word used, the tone, and the context.  However, neither is able to understand geopolitics enough to debate it.  At Int 3, it understands the basics of speech.  It may not be able to vocalize, but it gets what many words mean.  I see this akin to knowing about 1000 words.  (By comparison, an average person can know 25000 words, including derivatives).  So your animal (or special needs cohort) might have a limited understanding of conversation.

However:  A bonded companion animal, like most animals is highly attuned to empathic signals.  They detect pheremones much better, and so on a purely emotion level, you have a deep connection.  This gives the int 2 critter the ability to respond emotionally to your needs.  (For example, if you seem famished, a pet hawk might regurgitate it's meal for you, thinking that it is doing you a favor.)

In the same way, an int 3 critter might have a little bit mroe reasoning.  "Human does not each puke.  Should get rabbit instead."

2) When can an animal vocalize back?

Almost never.  However, with the right kind of magic it could happen.  I'm thinking of something like permanent tongues.  Why?  Because magic.

Han Solo understood the wookie language, but could not speak it. He was not able to manipulate his voice into the growls and roars that the language needs in order to be understood.

An animal with a 3 intelligence is only half as a dumb as the dumbest possible PC in our point buy system. You could have a character with a 6 with an 8 in point buy and a -2 racial trait. Is it the smartest thing? no. can it reason? i think it can. 

"master is attacking front, i attack backside." Manipulation of basic instincts like a wolf pack flanking is not outside the realm of possiblities. You wouldn't make a handle animal check against a dragon with an intelligence higher than two as it is considered intelligent. You would use diplomacy. I would argue you that if you were making a check against an intelligent animal, it would need to be diplomacy. An animal that is a friend or companion however, would not require handle animal as it is going to want to help you. I also dont think it would require tricks, as we have already said it can reason.

Keyes - I don't think this is about attack tactics per-se...It's more about being able to converse with the animal.  I don't think anyone has an issue with the wolf attacking from flank (since most pack animals do that on their own.)  That's where the term "Wolf Pack Tactics" comes from.

As for dipolomacy vs. Handle animal for companions, I strongly disagree with changing that mechanic.  To be blunt, it jams a stick in the pooper of the Druid/Ranger.

First, Diplomacy is cross class for both the Druid and Ranger, while Handle is a class skill.  So that's a 3 point swing, or 15% success rate.

Second, look at the ability called "Link":(

Link (Ex): A druid can handle her animal companion as a free action, or push it as a move action, even if she doesn't have any ranks in the Handle Animal skill. The druid gains a +4 circumstance bonus on all wild empathy checks and Handle Animal checks made regarding an animal companion.

So if it all switches over to diplomacy (which the rules don't say to do), the druid and ranger lose a net +7, and they lose action economy (free action to handle, vs. what I assume would be a move or standard action?).

As for tricks, my interpretation of the rule for projecting tricks beyond int 2 is that at int 3, you get 9 tricks, and at 4 int, you get 12 tricks.