I don't think anything that Monolith has made can beat the original Metroid Prime but since the question is about whether Monolith has surpassed Retro and the fact that Metroid Prime is now 13 years old, I think the answer may be "yes." I'm afraid that Retro may no longer be capable of making a Metroid Prime quality game anymore and that's why they are being given less ambitious projects (in my judgment, a 2D DKCR is less ambitious than a 3D Metroid). Also, it's well known that a lot of the talent that made Metroid Prime is now working on Halo at 343 studios.
Now it's possible that Retro has been able to replace this talent but that remains to be seen until we see them work on a project that really pushes the envelope the way Prime did. Tropical Freeze may be a good game, but it's not new territory for Retro Studios and it isn't something that would win them the title of being Nintendo's AAA studio, in my opinion.







