Wow that is quite a big dose of questions that were left unanswered for you. That was one down side of FF XIII that a lot of things still needed to be explained even after getting very much through the majority of the game. Here is what I can offer:
3) If Barthandelus wants Cocoon destroyed and Orphan wants to die, why do they do their best to try and kill you throughout the game? If they want to die, why don't they just tell you they want to die and get it over with already? Why do they put you through so much trouble if they just want you to kill them. All of their mind games seem so unnecessary if all they want to do is to die....
Yes Barthandelus wants to destroy Cocoon and bring about Orphan so that they can die and bring about a so called Apocalypse but they can't just let the party kill them. They were playing mind games and tricking the group the entire time to make them believe that their true focus was to destroy Ragnarok, not to destroy Orphan. They need the l'Cie to become Ragnarok and then destroy Orphan which would bring about the destruction of Cocoon.
16 Why can't the Fal'cie carry out their own actions? Why do they need L'cie slaves to do their work for them? If they are half-gods they should be able to do anything they want, right? What's stopping them?
Orphan said it himself/herself that men have unlimited potential. "Men dream, aspire, and through indomitable force of will alone achieve the impossible." So by using l'Cie they are taking advantage of that unlimited potential that all humans have.
20) When Fang and Vanille become Ragnarok during the ending and save cocoon by wrapping it in crystal, I assume this means they completed their previously failed focus from 500 years earlier? I thought their focus was to destroy it, not prevent it from falling?
Their focus was to become Ragnarok and destroy Orphan, but as Lightning said in the moments before the last fight "You gave up on life before you were even born. Sat poisoning Cocoon from the inside waiting for someone to come and destroy you. All you care about it death's release, so take it and leave the rest of us alone. We dont think like that. When we think there is no hope left, we keep looking until we find some. Maybe Cocoon is past saving, but we'll protect it or die trying. We live to make the impossible possible! That is our focus!"
So pretty much our new focus is to save Cocoon, not destroy it.
21) When Fang and Vanille enter crystal stasis AGAIN after becoming Ragnarok in the ending cutscene and stopping Cocoon from crashing into the ground, doesn't that only mean they will wake up from Stasis in another few-hundred years and it will just fall anyway?
No, they failed their focuses last time so they were made into crystals as punishment in a sense because the fal'Cie knew that Fang and Vanille were needed to become Ragnarok but it wasn't they right time for them. Now when they became crystals it's because they fulfilled their focus, they won't be coming out of that crystalysis.
24) Is your party really turned into Cie'th before the final battle or is that just more illusionary tricks from barthandelus?
They are for a moment but it turned out just to be more fal'Cie smoke and mirrors like Sazh said. They were in the darkness of the Cie'th but were pulled out of it.
25) After Ragnarok wraps Cocoon in a protective crystal barrier and stops it from falling during the ending cutscene, all of your party members appear to be in crystal stasis...then magically they're not all of a sudden...what gives?
Fang and Vanille talking to the party after the came out of crystal state explained to them that it was the last thing that they could do. They saved Cocoon from being destroyed and were giving the 4 party members as well as Serah and Dajh a chance to make a difference in the new age of Cocoon by drawing them out of their crystal state.
I'll try to answer more later, that typing was a lot lol
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