Here is the problem with the Star Fox series. Each game has been developed by someone different.
The first was a co-development project between Argonaut, who handled the technical programming (because Nintendo was as yet unfamiliar with 3D development), and Nintendo handled the story, music and game design. Star Fox 64 was entirely an in-house Nintendo affair, which to me is why it was so much better than the original. Adventures was not a SF game to begin with, Nintendo had Rare slap SF characters in it because they thought it would make Dinosaur Planet sell better. But with the exception of a couple of half-assed space levels, the game was just Dinosaur Planet. Not a bad game, but NOT Star Fox. Assault was a sick-joke, and that was entirely on Nintendo for allowing Namco to develop it. I was so stoked for that game, and then it came out and was one of the worst games I've ever played. It's literally the only game I've ever played where the first two levels were very-near-amazing, and the rest of the game was one, long, painful, soul-crushing experience in disappointment.
As for Command, on paper it wasn't a BAD idea, but in practice controlling the Arwing with the touch screen was a HORRIBLE idea. The moral of the story, ultimately, is that there are some franchises you can get away with "experimenting", such as Mario, and then there are some in which you really just can't, such as Star Fox. There are some franchises where the phrase "If it ain't broke, don't fucking try to fix it" rings true.
The reason every "Star Fox" game since SF64 hasn't been all that good, is because none of them since have really BEEN Star Fox. So hopefully, if they (god willing) give it another go-round on Wii U, in HD, they learn their lesson, and just make a STAR FOX type game. It's totally okay in this day and age to still make a game that JUST consists of space shooter levels, with perhaps a couple tank/submarine levels thrown in to mix it up. Star Fox was good BECAUSE it was a 3D on-rails arcade style shooter. Mess with that, and you mess with what made the game/franchise awesome in the first place.