Flores' bat was behind because we picked him up as a rule 5 and he skipped two levels. 09 was a heck of a start before his shoulder fell off. This is a guy who, while playing at the MLB level before ready, put up 2.3 WAR in 627 PA and had put up a 0.9 WAR in 09 in only 106 PA. His 09 BB% was around where his 08 AAA BB% was which indicates a 24 year old learning to hit at the MLB level. He had some pop for sure. 20 HR in A+ for the Muts before we picked him up. 8 HR in 301 PA in 08. 4 HR in 106 PA in 09.
His BB% in 2008 AAA is irrelevant because he only had 69 PA. That is a very small sample size. BB% doesn't stabilize until 200 PA. http://saberlibrary.com/more/sample-size/
That means he would have needed about 3X the PA before we had any idea about his BB%
Not sure how you conclude he has a weak bat. Wil Nieves has a weak bat.
.313 OBP and .719 OPS in the big leagues and .309 OBP and .740 OPS in the minors.