In fact, the only thing Team Flash really had going for them against the Thinker was the fact that the Thinker’s body was degenerating at a dangerous pace and he was doomed to die sooner rather than later.
The Thinker has been messing with Barry and Team Flash throughout Season 4, but it was never clear what exactly he was planning.
Team Flash could have theoretically waited him out.
His high-tech chair could only keep him alive for so long, and he was on his last legs.