I recently watched the SF Debris review of Star Trek and he spent the course of four videos mercilessly pointing out all of the flaws in the story. At the end, he gave it a 7/10 though, because, despite all of these problems, it was fun, and overall it worked. Which was the exact opposite of his criticism of Nemesis, which he felt took itself too seriously.
Yes, Star Trek could have been improved, for the reasons you state and more. And, yes, I do hope they fix some things in the sequel, but overall, if I walk out of the sequel every bit as happy as I was after watching Star Trek, I'll be happy. I recently re-watched it, as it's quickly becoming one of those movies I can re-watch over and over again.
As for plot holes, yes, it would be nice if they could avoid those, but sadly, it seems every big-budget movie is filled with them. I'm far more forgiving of plot holes if the movie works and I am enjoying myself.
I personally don't have a problem with the bridge and I actually like it. And while the bridge on the Kelvin was nice, in color scheme and aesthetics it reminded me of the other bridges we've seen on Trek. The Enterprise bridge in this movie stood out as something different, and yet it still was recognizable as a Trek bridge. And I absolutely love the idea of the window viewscreen.
While some are calling it the "Apple Store" bridge, I think that's a compliment for the set designers. All science-fiction is a reflection of where we are today and our ideas of what the "future" will look like. Apple has positioned itself as an innovator and many view their technology as the pinnacle of what our society can produce (and I'm saying this as a PC/Android man, myself). For better or worse, we tend to look at the Apple design aesthetic and think "futuristic." And choosing white is a clear nod, in my mind, to Star Trek's optimistic view of the future. We think of white as being "pure" and "bright," which I think matches nicely with Rodenberry's view of the future, one in which we evolve past our mistakes.
The lens flare and shaky cam are a matter of opinion. Honestly, while it's an easy target for humor, I really only notice the lens flare when I'm looking for it. Again, I think it's an extension of the idea that this is a relatively "bright" future, compared to the dystopian view of the future we so often get in science-fiction.
As for engineering, I'm in the camp that is not a big fan of it. I believe it was in the SF Debris review that he said he didn't have a problem with it, because he felt the engine room should look more functional. From TNG through Voyager, Starfleet engine rooms resemble more computer hubs than actual engines. I can see his point, but I don't think the pipes were the way to go. I actually think Enterprise had a decent idea of the engine room. It was clear what the engine was and the room itself looked more functional. Anyway, I if I recall, we have been told they are filming at the Budweiser distillery again, so it's not likely to change for the second movie.
While I disagree to various degrees with most of your complaints, I still think some of them have a bit of validity to them. However, it really doesn't matter, since most of the decisions have been made already. Sure they still have time to fix somethings, but I doubt they have time to fix sets or major plot elements.
Again, if they end up making as enjoyable a movie as the first one, I'll be happy. Warts and all.