How to work with an overly positive advisor?
I sympathize with this because I had an overly positive advisor for approximately 3.5 years, until I was getting ready to go on the job market and then suddenly he had tons of problems with my work. Others have told you to go elsewhere for criticism. This is probably a good idea, but you should also be able to have a good, balanced discussion with your main advisor who knows your work best.

Two things might be helpful:

1) Ask her what criticisms a reviewer might have of your approach to X

2) Ask her what needs to be done to improve Y

The first may help because she may be able to get in a different mindset about criticism if she is asked to think about the paper like a reviewer (a reviewer's "job" is to be critical, but she may feel that an advisor's "job" is to be encouraging). The second may help because it invites her to frame problems in an encouraging, positive way (which seems to be her comfort zone).