In response to OP: The idea behind the three policies is they are follow-ups to the initial counterparts - Freedom is a good follow-up to Tradition (Tall empire), Order is a good follow-up to Liberty (Wide empire), Autocracy is a good follow-up to Honor (Warmonger empire). This is overly simplified, of course, it is quite possible you might switch styles during the game but it is the general idea. Thus, Freedom, Autocracy and Order all reflect completely different empires.
Now, as to whether Freedom is too strong and the counterparts too weak: No. For several reasons.
First of all, Freedom, being focused on specialists and great people, benefits small empires far more than large ones. If you are running a truly vast empire, it makes little sense to adopt Freedom. Wide empires typically have less developed cities with less population and less infrastructure (and associated specialist slots), not to mention fewer wonders, all of which are factors which mean less specialists. A small, tall empire is much more likely to be generating a large number of great people points - in cities with wonders and good multipliers for those, such as the Garden and the National Epic. It is far more useful to be generating great people in a such super-city than trying to do so across a large number of underdeveloped cities. That is one of the main reasons why Order is a better choice for a wide empire.
Beyond that, Order makes sense for several more reasons. Nationalism and United Front are some of the 'crap you have to go through', I suppose. They are crap, in a sense, but at the same time they really aren't. The reason why I say this is it's true you may not need them against the AI. But is that a problem with the policies? No. That's a problem with the terrible AI which you can beat with hands tied behind your back. Both policies are in fact incredibly useful for defending your empire - it's just the fact you're playing against the underpowered AI that makes you think otherwise. In that regard, you might call the Freedom policy Universal Suffrage 'crap' as well, because you'll be able to defend your cities just fine without the extra strength. In multiplayer, though, or against a possible future working AI, these policies are invaluable.
The case is the same for Autocracy. In my opinion, Autocracy is not weak, no, it is in fact one of the most powerful trees in the game. The Autocracy opener alone is the single biggest economy boost in the game. The unit cost reduction beats anything else hands down, including Freedom's Free Speech.
Beyond that, the rest of Autocracy is pure awesome. Populism gives you a semi-Bushido unique ability for your whole army which will make the difference between victory and defeat in close battles (read: Non-AI battles). Militarism is, once again, one of the biggest gold-boosters in the game. Fascism enables you to have a much larger army than anyone else (which you'll need!). The new Police State policy is likewise one of the best happiness boosters in the game. Total War received an insane boost, enabling you to have not only a much bigger army, but a much *better* army as well. As such, it would be idiotic to try for a domination victory using Freedom. Order could possibly work, and Autocracy would be ideal. Order is more geared towards a somewhat peaceful approach, however, which is why its military policies are defensive in nature. Probably better suited for a science win.
Now, once again, despite how absolutely awesome Autocracy is, it runs into the same problems as Order: You don't need a large army against the AI. You don't need lots of upgrades and special abilities for your army. You'll beat it easy anyway with just a fraction of the number of units the AI has. In that sense you are right, Autocracy 'stinks'. But you're delluding yourself if you think that's the truth. Reality is the AI stinks, not the non-Freedom policies.
