They likely got to work on their own IP for the first time since they were bought by Nintendo. Back then they had four games in development, but Nintendo stopped them all and had Retro make Metroid Prime. Perhaps the whole studio never had and will never have what it takes to make a new IP that is fun. After all, the developers that left Retro over the years have also only produced disappointing titles.
So the new IP that Retro had been working on never managed a turnaround and years of work amounted to nothing. That doesn't mean the studio can't produce quality games anymore, but rather that they are reliant on existing IPs to develop something worthwhile. That would be very similar to Inti Creates who do a good job with existing frameworks, but are terrible with original work.