Middleton was still a very powerful owner - he was behind the ouster of Giles in favor of Montgomery, and was obviously in lockstep with Montgomery when it came to trying to squeeze a few more years out of the '08 core, from the Howard contract to re-signing Utley/Ruiz/Rollins to adding Papelbon and Burnett when Halladay, Lee and Howard were zeroing out. But all you can really blame him for is not forcing out Monty sooner, and unfortunately that required a cancer diagnosis.
But yes, it takes 5-6 years for farm systems to bear fruit especially if you are drafting high school players. The 2016 draft is a lose-win at the top (Randolph/Kingery) so far. Moniak is still incredibly young and Haseley has passed him by virtue of being a college player. I do think Klentak was not aggressive enough with the overhaul given he inherited a franchise picking 1-1, but you can't really magically create an analytics department in 6 months either, when your predecessor didn't have one at all. The flawed players on this year's team are mostly guys he decided were still worth having, i.e. Franco, Herrera, Eflin, Pivetta, Eickhoff, Williams, Quinn, Knapp (only Velasquez is one of his).