Awfully weak story... or is it? [WARNING:SPOILERS]

[Alberel]

Most of these points were actually explained or made obvious enough that you could work it out.

-the ascians: first, they didn't tecnically betrayed the empire. Ultima was their triumph card, but Gaius never wanted bring such devastation. He wanted to rule over a reign, not pulverizing. However, the reasons why the ascians deal with the empire it's still unknown, and for now even contraddictory: they stated they need the power of the primals, but they helped the empire which goal is their annihilation.Why, it's still unknown

The Ascians were manipulating the Garleans into feeding the Heart of Sabik (Ultima's core and power source) primal aether. Primal aether is what it uses to cast Ultima. Ultima is seen to be so powerful that Hydaelyn cannot defend against more than a single blast from it therefore it's fairly safe to say that Lahabrea wanted to use Ultima to decimate Eorzea and weaken/harm/destroy Hydaelyn in the process.

We still don't know what the Heart of Sabik actually is but Lahabrea implies that it is an ancient Ascian device of some kind that they tricked the Allagans into using when they first constructed Ultima Weapon.

-also, they stated the balance will be ruined forever if Hydaelyn would be allowed to live. What balance and why ?

The balance between light and shadow. The Ascians have a link to the void and I'm pretty sure it's actually the 'shadow world' where the dark crystals (and warriors of shadow, assuming the game follows the motif established in FFIII) reside. The THM quest line explains that powerful voidsent cannot move from the void into Eorzea easily and instead must send their aether through to possess a host. I'm pretty sure the Ascians are doing the exact same, and are in fact simply VERY powerful voidsent. (Chances of the void being a future expansion focus are pretty damn high I think.)

Lahabrea suggested earlier in the story that Hydaelyn had previously done something to transform the world from it's natural state so the Ascians seem to be retaliating against something she did. We still don't know what but it seems she isn't as 'good' as we're led to believe.

-In the cutscene after the credits, we see more of the soon-to--be-released ascians overlord. In their world, they again say they need the primal for awaken the only true god: zodiark

They're still somewhere in Eorzea, Lahabrea has just taken on a new host. It's also worth noting there are twelve of them. We also have twelve gods and Dalamud was held together by twelve swords. The number twelve is clearly important.

-In praetorim, Gaius hit the mark: the Twelve we worship don't lay an hand in our help, unless we enpower them with aether, just like the primals, and like we did in 1.0 to prevent the descent of Dalamud (failing). Is it possible we are doing it wrong and worship an evil ?

There are lost of theories in the lore forum about this one. We don't know for certain but there are many many hints in the game that the twelve are not truly gods. Even the FSH questline makes a subtle hint that The Twelve are little more than exaggerated folk stories in their level 50 quest. Considering all magic in Eorzea is simply aether given form it's not too hard to imagine a very large amount of aether could take on more... permanent forms.

-Always on Hydaelyn, in the cutscene before credits we see with the Echo a purple Hydaelyn. A second mothercrystal? A corrupted Hydaelyn ? In the next story missions, we'll know for sure.

The dark mothercrystal is Zodiark. Somehow the echo that lets us commune with Hydaelyn also allowed Zodiark to briefly make contact with us. Interestingly it happened as Bahamut awoke, which implies Bahamut's power is somehow disrupting whatever force is sealing Zodiark away. You can see now why the Ascians wanted to release him...

Anyway back on topic I thin this post makes it pretty clear that ARR's story is far from weak. The storytelling itself is average to good but the lore, history, setting and subtleties are actually very very complex. The thing is here that the main quest only gives you a vague overview of the story. A great deal of hints and clues as to what's really going on lie in some of the class and job quest lines.