Actually, for careful people, the story have setted the base for a lot of side-points to be expanded. I'll talk about this later. Meanwhile, i'll take the time to respond to some points:
on Gaius:
-he is all you said, but still, as you said, it's a conqueror. It's someone who believe what he's doing is right and everyone else it's wrong, and that don't make him a righteous.
-The garlean empire it's far from being a good empire: his emperor it's driven by the conquest, and new territories are made one of them using indoctrination and coercion. This is better explained in 1.0.
-Gaius didn't really offered a peace because it's a good guy: with a monster like the Ultima Weapon in hand the defeat of the city-state would been inevitable, and it was a way to force them to surrender without fighting. Mind you, even we players, if we didn't got "blessed" by Hydealyn would stand a chance. (quotes: read further below)
- isn't a stereotype of a bad guy, but the kind of "different sides" villain: he have good and bad sides, but the fact endangers our home as a foreign conqueror put it as a bad guy, and it's our duty stop him.
-the purpose of Gaius seems noble: conquer Eorzea, purging it by its false gods, and give people the stability they always wanted- at the cost of freedom and their soul, even if Gaius think otherwise
-grand companies:
-I don't know what point you're making in the first sentence
-the primals are powerful beings, and very few amoung men can defeat them face-to-face. Also, it's stated the grand companies are in grave shortage of men: in these 5 year since the Calamity, grand companies and city-states has been busy rebuilding. they couldn't waste time dealing with beast tribes and garleans, that's the reason the territories around them have so much garlean stronghold around. (Expantion: the primals are so powerful even the very same Garleans can't take them lightly. Their advance of 20 yeasr ago was halted by the threat of the primals, or else at this time we would already been conquered)
-And what's the problem about the generals don't ben the lords of the city-states? They are soldiers, not politicians, also it's not that accurate: the Admiral it's in fact the rovereign of Limsa Lominsa, not so sure about Kan-e-Senna. The only i'm sure it's Raubahn, for obvious reasons: the Sultana reign over Ul'dah, even if true power is at hand of the Syndicate.
-wrong: since 5 years they don't do else then helping rebuilding.
-This is hilarius, sorry. The fact we are supposely good don't mean we are fools. The garlean empire alone it's a terrific power, plus an abominion as Ultima Weapon, and maybe more from Lahabrea. Do you really this it would be a wise choice taking an army full of robotic machinas, war airships, and gun-weapons head-on, while the best we have is some magick and a pick on a stick ? please, tell me more.
-read better, they are not ignoring nothing: they know their problems are still there and they have still lot of work in front of them. But they got the evidence if they work united as one they can overcome everything, even an invincible enemy. That's the message the story send.
Now, as i said, there's a lot of hints more or less hidden in the story, which hints of the futures stories: [MAY CONTAIN HEAVY SPOILERS]
-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
-also, they stated the balance will be ruined forever if Hydaelyn would be allowed to live. What balance and why ?
-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
-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 ?
-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.
-Take all these pieces together, and you'll understand there's something underway, and we could be doing wrong until now.
further edit: while for many it's the same game, this is both a reboot and a sequel: the story it's a following of the previous 1.0 and that may confuse new players who don't know about it