It could be that the writing and pacing problems were not as occasional as to be a quick fix. Particularly if the overwriting was seen as your writing style, as opposed to some fixable problem. I know that when I beta, it's easy to point out specific problems in the novel, & even more overarching ones like an unlikable MC, but if the writing in general doesn't match with my preferences or what I think the market wants, that can be a very frustrating problem because it's hard to articulate to the author what needs fixing or to even imagine the author being able to (or willing to) fix their writing style.
Of course I agree with others that even if those problems really were as minor as you think they are, the agent could just not have fallen in love with the book, despite seeing its virtues, and so she shared those virtues and some faults with the hope that you can improve it for some agent who does fall in love with it.
