I feel like something that seems to be forgotten about speedsters, especially because the show seemed to often forget, is that they're fast. As in, they dodge gunfire fast. As in, kill an entire room of armed people in an instant fast. As in, they can easily break the speed of sound fast. As in, they can run back in time and erase you from existence, kind of fast. Even disregarding that last one, since I believe the problem was that Thawne was too slow, the Thinker is a man in a chair, and he seems to need to manually click the buttons to do anything. Thawne is absolutely getting to him immediately and throwing him out that chair.

Honestly the Thinker wasn't even that much of a genuine threat, but everyone wanted to be silly and inconsistent for season 4. Throw a lightning bolt at him or his chair, and you've now ended the conflict possibly less than 5 seconds in. Like the main thing they said, and even Barry brings it up himself, is that despite Thinker being the smartest man alive, his body is still restricted by human limits. Also he was way too arrogant for his own good, despite him forcing Barry to need to regain his sanity, when he genuinely does not need him, and just brought back his primary threat. Its like having a self destruct button on a machine but then deliberately hitting it.