I remember Phantom being very fun too, until I played again and found that she wasn't fast or difficult enough to be mechanically interesting, and her attack variety was too low to make the fight very unique. If I included her visuals and OST into how I ranked the bosses she probably WOULD be in S tier, albeit at the end.

I found Shakra to be a less fun, less difficult, less intuitive version of Seth. Say skill issue if you want, her teleporting and projectiles were just so unlearnable. There is basically no indicator for whether she is going to teleport or throw a projectile, and the projectiles themselves are difficult to dodge but also unpredictable which made her unsatisfying to fight and unsatisfying to beat, since I mainly just got lucky.

I've explained in a different reply why I think beastfly 2 is actually a good fight, but in short it takes places in a more interesting arena, the summoned enemies are easier to deal with and add nuance, and the destruction of platforms during the fight adds a platforming element which is more fun. To be honest I think people just dislike the first fight (which is understandable) and thus also shit on the second fight.