Confession: I've beaten Final Fantasy XIII three times and I still could not tell you what's going on during the final battle sequences. It's basically just "So I'm supposed to kill you now, right? Okay, sure whatever."
My understanding was that the Space Pope was secretly a Robogod trying to kill an even bigger god so that he can be with his big mama god and he wanted Miss Amnesiac to go super sayin again to wreck the Death Star and crash it into Namek thus waking up big mama god and thus sends the merry band of misfits down to Namek to powerlevel for a while, they come back and bring an assload of Namekian fauna with them, Robogod pulls some bullshit to insta-turn everyone into zombies, your guys fumble around in the eleventh dimension for a couple of hours fighting a couple dozen doomstacks of HP, you make it to the Robogod and fight him again, he dives into a pool and becomes the bigger Robogod that he's trying to kill, you fight him again, you win, you still lose, your party gets turned into zombies, the Thunder-from-down-under goes super sayin, bullshit happens and your party gets Holy Water'd by big mama god, the Aussie lesbians perform symmetrical docking and go SSJ4, they kill Robogod mk2, then they pull a Superman and spin around the Death Star enough times to turn them and it into a big fucking PSN Trophy, everybody else ends up on Namek and live happily ever after (until XIII-2 which immediately retcons that into Miss Cloud disappears for no real reason, Little Miss Serah-chan makes puppy dog eyes, Mr. "I'm a Hero" disappears, then Gogmagog shows up and gets jobbed by KH's Sora using the bulletproof alias of Noel Christ).
I just love describing that sequence. Its just such a useless clusterfuck of Deus Ex Machinas, outright bullshit, complete and total comprehension failure on the characters' part, complete tonal dissonance from the Logan's Run plot up until the endgame sequence, and the complete and total uselessness of the party barring the two who are, for all intents and purposes, the real leads of the game (which is why Fang was supposed to be male because Japan can't seem to have female leads without a male lead stealthily becoming the main character and/or stealing their thunder).
I guess this is where we're just going to have to agree to disagree: I hated the battle system in XIII. I've ranted about why at length before and I don't feel like going into again. But when you take away the battle system for XIII...what's left?
Kinda falls into my beef with the trilogy thus far as well. For a series of Triple A+ developed games, they barely feel mediocre at best. I've gotten more out of Star Ocean 2 and that GBA Tales of Phantasia port than either FFXIII games thus far. They feel like Breath of Fire 2 with the cliched archetypes, the unbalanced and gimmicky battle system, the grindy endgames, the backtracking (in FFXIII-2's case), and especially in their plots which are just as comprehensible as BoF2's plot after the shoddy localization got through obfuscating it (though one difference is that BoF2 has much better character and enemy designs).