I know it is kind of a stretch, but all the impossible feats we accomplished like taking on primals, the empire, and other major feats were done with a party, not just you alone. Even in cutscenes, the NPC's mention you need to gather your companions and go in and fight.

Look at previous Final Fantasy's. FFX for example, you have taken down major sinspawns and other major enemies, but you are still running from Seymour's guards to escape. I know it seems ridiculous that our character seems like he is against normal soldiers, but in a story perspective, being surrounded by a bunch of swords to your neck and going guns blazing instead of being handcuffed would make you look more guilty.

Not saying this was the most well written thing ever, but sometimes this is just a thing. This logic has been done so many times in various games.