In a word, Questlove.
Tariq basically hitched his wagon to that live band/jazzy type steez that was dope in 92-94, but mostly done by 95. Digable, Buckshot Le Fonque, Jazzmatazz, US3, etc came and went. Gangstarr moved on but the Roots didn't.
The Roots stayed on that sound, period. Maybe they changed a little during Illadelph, but by and large they have always been on that "Sunday morning clean the house" style. So if you were into that Neo Soul scene, that's where they were. That was their lane.
So Thought's destiny was tied to whether or not you liked The Roots. And most folks thought the sound was cool, but not banging. Their biggest song might be You Got Me, and if that was anyone other than Erykah on the hook, I doubt they would even have that.
They have always been dope in terms of live shows, but it's sort of on some Dave Matthews Band vibe. Grown up when the market is teenagers and young adults.
The fact that they toured 9 months out of the year for decades also needs to be taken into account. If Thought did more guest features. But few wanted to be associated with his grown and sexy vibe.
So he's not in the conversation based on his aphiilyation.
And tied to that, he isn't good at picking beats. All his solo joints might have a good song or two, but a lot of the beats are just boring and generic. So even when Quest is not involved, he still picks Roots type beats. El Michel affair is a good example of aight beats, but very few bangers. Cheat Codes, Streams of Thought...
He can flow over everything, so he just flows over anything.
Skill wise, he can't be denied. But being a great mc is about more than skills.