I appreciate that you actually gave time to the game and made a long and detailed write-up of your opinion on the game's flaws.
However I just feel like your primary complain falls flat to me. The game color codes
everything for you, your current leader is always surrounded by a bright circle, so it's really hard to miss. The game punishes you by getting hit in the way of all your characters getting spread around, so it emphasizes defense as well as offense.
I never really had a problem with telling what was going in the game, and I played the entire thing with Off-TV screen. Those (admittedly annoying) sections where you have to watch both screens at the same time, I had to do this with an even tinier screen on the bottom left of the gamepad screen, but I didn't really have any issue telling what was happening, one just simple has to pay attention.
I also disagree with the battery mechanic complains, I think it actually complements the battle system really well, as it adds a layer of resource management that shines better in the higher difficulties.
That said I do agree with the mini game complains, I really didn't have much fun with any of them except the glorious
and that one high-speed section on Operation 2. I like that they diversify the game, and add some nice pace to it, but I don't think they are all that really well made, it's specially annoying that they are taken into account for your rankings.
I also agree somewhat with the story, I love how silly and over the top the whole thing is, and how it doesn't take itself too seriously, but I do agree with how some of the portrayals of the characters got annoying, like Wonder Pink, and Wonder Green (and by extension, Blue's interactions with Green)
That said I still really love the game, it's my favorite game of the past year and possibly one of my top 10 games ever, I can understand why the game is so divisive, but I just don't really think some of the criticism the game gets regarding it's gameplay are fair, but different strokes for different folks, I guess.