Outside of the confusing story branches, I like the way the story is paced. Even most of the slice of life segments ends with some kind of dangerous element, that make it feel like a series of mini-climaxes, instead of one big twist like the first game. Also, the second half of the original game was so strong it almost made me forget that it was REALLY difficult to get past those first several hours, when Kyouma was too obnoxious and I hadn't gotten to like the characters yet. This one starts off pretty much immediately, which I appreciate.
I remember that the Japanese release was delayed a few weeks to fix up quality issues or something like that. I think it could've used a few more weeks more to make some things clearer and expand on the true ending. One of the main premises is Okabe going through all of this to save Kurisu...so maybe some extras scenes (beyond the Amadeus stuff/"dream" sequence) would've been really helped it out.
Some things are still messy regardless, especially anything involving Kagari. There are, what, at least three different variations on the character? It's hard to feel for her when it's so confusing, especially since, by nature, her character is so malleable. Also, I found her adult design really distracting - I thought she was basically vagrant by the time you meet her, so why is she wearing such fancy clothes?
Initially I thought the story would focus more on Okabe's interactions with Amadeus Kurisu and World War III, but the story really only skirts with these (or sticks them in the beginning) and instead focuses on Kagari. Plus, what's the deal with the encephaltis breakout? It was brought up in that branch and then dropped. If this is meant to be sequel bait, I'm not sure if the questions being asked here are really worth a whole new game to answer - it feels more like sloppy writing.
Considering the whole game was about the steps to reach Steins;Gate...there are really only two main things, right? Okabe learning that he can "fool the world" (which is still a concept I'm trying to grasp...it made sense due to the casualty loop in the original game), and Mayuri going back to tell her past self to slap Okabe. It seems to imply there are other, untold branches that lead up to the true ending...but none of the endings really "go" anywhere. I love them (especially Maho's branch, which is one of my favorite parts of the game), so I wish they contributed more to the overall story.
The other aspect I really liked was Mayuri's development. In the first game, she was basically just a puppy dog that existed to get kicked around by the universe, but here she's a much more interesting, motivated (and less air-headed) character. Some of the character arcs could've been handled better - I like Daru's development but there's no real moment where you see his growth - he's just struggling and then, you're in the future and he has his shit together. The story also has no idea what to do with Luka and Faris, which is fine, except for when they kill Luka in an extremely melodramatic, pointless manner (doubly check because they don't show any of the aged characters except Daru). I heard similar complaints with Moeka, but I enjoyed her presence in the Maho branch.