Honestly, when I first finished the MSQs, I felt sort of indifferent about them. However, after thinking about it more, I actually like the way it ended.
I didn't really care for the part where you fight ElidibusZenos as Hien. However, seeing your character arrive from his perspective was neat.
Indeed the MSQs did leave more questions than answers. However, I feel like that's supposed to be intentional. I feel like Stormblood did a good job of reminding us of the warrior of light's humanity, that he/she has limits like everybody else. All the small moments in these MSQs also remind of this, like Tataru crying when she sees your character, and Aymeric rushing to your side when your character awakens. I personally felt emotional after waking up in Ishgard.
It feels as if all these moments were a reminder that all the friends your character has made, all the light and life your character has known, is about to be broken. Since the fate of the called Scions is unknown, you must go forth alone. The last scene overlooking the Crystal Tower sort of felt like a sendoff. So perhaps it isn't quite as dramatic an ending as ARR and HW, but in my opinion, a good ending nonetheless.