1. Animation
It's interesting because there are plenty of moments where the animation looks completely fine, where it obviously got some necessary finishing touches. So it's not that they don't know to add those finishing touches or don't have the ability. It just didn't happen sometimes.
I do love that it accidentally resulted in Izzy looking tired for a bit. A person could just be tired. The story doesn't need to give a reason for it.
Zipp
They really did not give a good reason for Zipp to keep things to herself for so long. I suppose we could chalk it up to a bad habit she just hadn't broken yet. Prior to the movie she lived a very insulated and controlled life. It's possible she got used to her concerns not being heard so now she has a hard time sharing them.
Hitch
Hitch is a strange character. He's a parody of The Ace. He's the top (and now only) cop in town and is supposed to be awesome and looks great in the calendar pictures... but it's a peaceful town and he doesn't actually do anything important. He takes his job super seriously because he's bored, in contrast to Sprout who doesn't take the job seriously because he's bored. Hitch leaves the beach because he has absolutely no idea what to do. He's not actually that good at the job.
Unless someone he cares about is in danger. Then watch out.
Posey
I like to think Posey is just that mad about her flowers.
The script actually did answer her objections. Earth ponies just felt left out of this whole magic upgrade. They didn't know what they got out of it. Now they do.
The dragon
I don't know why, but I like that the dragon had no involvement in the plot.
The Plot
Yeah the plot is kind of a mess. This is exactly what first draft screenplays often look like. It's full of plot threads that don't really go anywhere, and there's scenes that could be combined for efficiency. It's just the beginning stage of a brainstorming session turning into a story.
I like it though. Maybe it's just because I'm a movie nerd that reads early screenplays for fun and can appreciate the weirdness of this, but I'm not philosophically against this kind of inefficient storytelling. The characters don't know opening credits have just played and it's time to get a plot in gear. They're just doing their thing and trying to adapt to events as they happen.
Songs??
The music was one of my few solid complaints with the first one, so I'm okay with this.
But I would gladly watch the director's cut if it turns out there was a bunch of songs cut from this. I'm always curious to know what the intent was even if I'm fine with the final product.
Sprout
Headcanon:
He's still watering those plants and that's where he's been this whole time.
Also, still a hundred times better than “War for Cybertron”, lol.
Easily. This was flawed but it's a happy mood.