Loose threads

[Enkidoh]

I think most of that simply boils down to the fact that much of the story (particularly concerning Zodiark, Hydaelyn and the Ascians) hadn't actually been developed in ARR beyond Hydaelyn being the 'good goddess of the planet" and the Ascians being generic doomsday villans in opposition to her that wanted to restore Zodiark for some nefarious purpose. But I'll try to answer what I can:

1. See above. It's possible SE were setting up Zodiark as being an opposite to Hydaelyn as far as the Mothercrystal was concerned back in ARR, but SE just never took it further (apparently a so-called 'Fathercrystal' exists underneath the battlefield for Zodiark in the Dark Inside on the Moon during EW, but I suspect that's just embellishment and not meant to be mean anything more).

2.That's pretty easy - Hydaelyn was calling out to her so that Hydaelyn could use her as a medium later on to speak to the WoL. Again this doesn't really fit EW's revelations about Venat however, so again it's an early story thing that never really was taken further (it should be noted also that Minfilia was desperate to learn about the secrets of the Echo and the Blessing of Light - she stated this in no uncertain terms way back in 1.0 - and was apparently particularly attuned to hear Hydaelyn's voice more clearly than pretty much anyone else, so therefore she was fully willing to give herself to Hydaelyn for that reason, even if it meant having to sacrifice herself in the process.

3. Put it down to the Garleans' 'might makes right' mentality (and something that Emet-as-Solus drummed into every Garlean). One of the stories on the Lodestone shows Emet basically browbeating Zenos as a young boy for his "weak body" (as part of Emet's loathing of Sundered life), so this would have undoutably had an affect on Zenos, making him strive for physical perfection even among the physically impressive Garleans.

And as others have mentioned, Zenos was drawing on the power of the katana he was wielding (it was speculated that rotating drum he kept his blades in was some kind of magitek device that infused them with aether that he could then draw on), giving him an edge against magic-using Othardian and Eorzean rabble he fought, and even allowing him to subdue the WoL, the 'champion' of the 'savages'.

There was that cutscene also showing Zenos having a nightmare of the Final Days of Amaurot, and his remarks was that he had been having that same dream since childhood, leading to some... interesting questions (was he actually a reincarnated Ancient like the WoL, as in possessed an Ancient's soul, or was it for some other reason?). Either way, it seems this plot point ended up being discarded or ignored and it was never taken further... A shame, as it might have given some further insight into what really made him tick.

4. I'm pretty sure that's just an oversight on the writers' part - Annoymoose had a thread where that was examined closely so I'll just point you to it for further information.

5. The 'Elidibus' that caused so much trouble throughout the game and was absorbed by the Crystal Tower in ShB (and sacrifices himself to open the gateway to the past in EW), isn't actually the real Elidibus at all - the real Elidibus was a youth named Themis (you meet him during Pandaemonium), who sacrificed himself as part of the summoning of Zodiark, with a construct in his form taken from his memories becoming Zodiark's 'heart'. The Ascian Elidibus that you see throughout the game is essentially a glorified primal made from fragments of the real Elidibus's soul and memories. His remarks are basically his Primal form suffering cognitive dissonance as his form breaks down following his defeat and G'raha deploying the sealing spell that sucks him into the tower's machinery, and his tattered memories begin to unravel (the words seem to refer to the seat of Elidibus being the Emmisary of the Convocation, in other words, a diplomat that mediates between disagreeing parties), so he was probably just reciting those words as more memories came to light.

6. Plot hole basically - although the Echo kind of ended up being a 'power that can be tweaked for a given situation or character', so that was probably just more of the same. Also the Ivalice raids were written/overseen by Yasumi Matsuno (producer of FF Tactics and FFXII) as I understand it so that might have played a part (an outside developer writing something that they don't fully understand about - kind of like how Gaia wielded a giant hammer during the Eden raids in ShB despite Tetsuya Nomura who wrote the raid story being unware that there was no 'hammer class' in the game and Yoshi just left it in for 'coolness'). Basically don't think about it too much.

7. Just a way of lore padding, fleshing out more of Othard as well as further underlining how awful the Garlean Empire was during SB. It's possible SE had planned to include Nag'xia in SB but anything that was written probably got thrown out long ago. Either way, if the XIth Legion still exists they've undoutably gone rogue since the Empire's collapse, and would probably just become glorified bandits in that area, cut off from Garlemald's supplies after all (not that the Garlean capital is in any state now to send supplies even if they wanted to).

8. Again, see my response for question 3.