I think StarFox Zero is a GOOD game and it does NOT deserve the reputation it has.
I understand the problem with this game's story being generic as it doesn't enhance the old 64 story in any substantial ways while failing to introduce any meaningful new characters. However, in a vacuum, the story is serviceable. I think the best thing I can say about it is that they didn't really misrepresent the characters in a way that I hated, which is more than what Command did, the last new StarFox game. What really matters is the gameplay, and honestly, I really enjoyed the gameplay here. Sure, we visit many of the same planets as before, but they do enough new with them to the point where the feel different. Here is the thing about the gameplay: if you are the type of person who plays through the story once and make a judgment then, then I think you are misunderstanding the intentions of the designers. I have no doubt that some of the most vocal haters of this game like Scott the Woz did that. The unfortunate thing about people like Scott the Woz and others is that their audience probably haven't played the game for themselves to form their own opinion, and thus assume the game is bad, which sucks. The thing about StarFox is that it is a game series where you are supposed to replay the levels to find new secrets and learn new skills to gain a high score, and I personally think Zero nailed this aspect.
Anecdotally, I played SF 64 3D as my first StarFox game way back in around 8th grade. On my first playthrough, I didn't fully understand the hype and thought the game was kinda mid. Thus, I didn't touch the game again for another year or two. During my second playthrough, I noticed that something was different this time. I remembered that I didn't play this one level and realized that I was taking a different path completely this time. I learned that there were many different routes over time and it made the experience much more replayable and it was exciting to learn new paths in this game. Furthermore, on this second playthrough I understood the controls more, and I felt like I was improving on old levels. Just like Mario and Pikmin, you can replay the same stuff again, but with enhanced skills, it gives me a new perspective. The point I am trying to make here is that Zero is basically the same way; the controls will take some getting used to after the first play through, but on subsequent playthroughs of these old levels will give you new perspective. You will find new secrets about the game that you didn't know about before and gain new skills that you didn't know about before. For example, I learned that if I held the L button, by charge shot didn't target anyone, and the radius blast could score me some extra bonus points. I also learned that if I shot down a ship flying in the skies, I could shoot the remaining debris for bonus points. Of course, there are the medals to collect and there are the different routes in arcade mode to keep the game surprising.
As for the controls, I think it was a bad decision for them to make the top screen's aim inaccurate. However, once you learn that most of the gameplay is only on the GamePad and that you don't need to look at the TV often during the on rails section, it becomes more fun. I think this Gameplay style especially works extremely well with All Range mode as you can see you is behind and all around you while aiming precisely as someone right in front of you. THIS is where the dual screen mechanic really shines. The original StarFox on SNES felt like it encouraged you to use first person mode for more accurate aim, but now Zero is requiring that as part of the control scheme, which didn't immediately click for some people.
Controversy aside, the game feels so smooth to play. The dual stick gameplay feels so natural and comfortable, and everything just feels so good. I really like how they enhanced the Arwing's move set by introducing the Walker mechanic. The game just offers enough new ways to control and a new level of freedom beyond 64 that I appreciate.
Yes, this is a flawed game. We could continue to dwell on the story, the graphics, and the controversial controls all day long, but at the heart of this game is a GOOD StarFox game and I wished that more people gave it a chance.