The man behind many fantastic Castlevania games was asked about if he would consider working with Nintendo on a major Metroid title. He gave the following answer.
“Nintendo is very careful about protecting their IPs and making any changes to their games. Around the time that I was proving that I could do multiple titles and do them well, Nintendo had shifted to Metroid Prime and they were having success turning their 2D games into 3D. So they probably decided from that point on that Metroid was going to be a 3D game series, and by that rationale, my style of games didn’t really fit their criteria. That would be my guess.”
It would be very interesting to see his Metroidvania experience work within the formula that Metroid series has followed (2D and 3D) over the years.
Source: NeoGaf