Bowden was the coach in name only his last few years, 2013 was Jimbo's team through and through. He left FSU because it had been allowed to become a shambles, not because he'd turned it into one. They weren't willing (or able?) to spend the money to keep up with the biggest programs.
As for what Jimbo has done at A&M, that has more to do with his inability to adapt to a changing landscape. Unlimited free transfers and a significant change in most offensive philosophies have left him behind, and even with A&M's resources he can't always out-talent the competition from week to week as he could in his early days at FSU. I criticize Saban a ton b/c he's always had the most talent, but he also has adapted his coaching style and his system over the decades to fit with his players and with changes in football in general. If Jimbo wants to win a Title, even an SEC one, or perhaps get back into the top 5 at least, he will need to adapt, as well.