I do think Logan is a more consistent and overall "less flawed" film.
Personally, I still prefer TDKR because it's more of what I look for in a superhero movie. An emotional rollercoaster with big spectacle and big emotion. And the ending is so bittersweet, yet triumphant. I walked out of the theater on cloud 9 with how beautifully that ending came together.
Logan nailed exactly what it was going for, but for me it's a bit more one-note and depressing. It's not a movie I see myself watching countless times, whereas I think the TDK Trilogy as a whole is something I'll continue watching for years to come.