Krystal's not a bad character at all, just inconsequential for the most part. People only hate her because A) Adventures-Command didn't live up to the greatness of 64, and she just happened to be there, and B) "Ew furries!" as if they weren't around during the previous games or something.
That said, 64 is my favorite of the series.
I think Assault is my second favorite, even though I prefer 64's map to Assault's chapter-based system. I didn't really have a problem with the land battles. I mean, they're kind of awkward at first, but you get used to them. And I enjoyed the weapon variety and what I consider to be the best multiplayer in the series.
StarFox on the SNES was what got me into the series, and it's still pretty good even though 64 improved on it in every way (except for the OST anyway).
Command is my 4th favorite. It gets a bad rap for its story, and I'm sure a lot of people had issues with the touch-screen based controls, but still kind of liked it. It has a bit of a steep learning curve, but it's pretty easy once you get the hang of it. Can't say I'm a fan of the character designs though.
Finally, Adventures is my least favorite. I'm cool with games trying out different genres, and I think it did okay. My problem was that it seemed very easy to get stuck. There was the hint system with Slippy, but for me they were never relevant to my immediate problem. And the ending was rushed too. However, it looks really pretty, even by today's standards, and it had my favorite design for Fox.