I don't think is it hypocritical, at least, not necessarily. But it can be a very fine line that is very hard to walk, and it requires a lot of self-awareness, and a lot of (for lack of a better phrase,) self-care.

Right now, having just started using MFP, I find myself going back to Kate Harding Fantasy of Being This a LOT. ( http://kateharding.net/2007/11/27/the-fantasy-of-being-thin/ .) Re-reading it, reminding myself. I also refer to her Reality v Realism piece ( http://kateharding.net/2007/10/29/reality-vs-relativism/ .) Not to discourage myself, but to remind myself that the success that I'm looking for won't be a number on a scale. That it's okay if I "go over" my calories. That when I have days like yesterday, where I hate everything and don't weant to leave the house, ever, and just want to curl up on the couch and eat cream covered pasta, it's okay.

My goals *include* a minor weight loss, because my cardiologist asked nicely. In reality, though, that's not what I'm really measuring. I'm food logging more to make sure I'm eating enough, and not falling into dieting traps that I've fallen into before. I don't own a scale, and I don't intend to buy one - the scale at the doctor's office is the only one I'm trying to please. Instead, my goals are increasing exercise, and increasing quality of nutrition - things I can set specific incremental goals for, and measure and succeed at on a consistent and non-arbitrary basis.

(for reference, the things I'm using as guides are these:
100 Day Experiment
http://us4.campaign-archive2.com/?u=34dc5132814738edbc8d54294&id=734a28d7eb
Exercise Ladder
http://www.fourmilab.ch/hackdiet/e4/exercise.html
and walking beyond what I do for work and transportation, working up to every day. Eventually I'll do a C25K.)

The one thing I would be careful of, in your case, is being conservative about the changes expected as regards weight loss and PCOS. I'm not a doctor, and I don't have it, so your experience trumps anything I have to say, but my understanding is that the hormonal changes that cause amenorrhea are more likely to cause weight gain than be caused by it. That is, PCOS causes weight gain and missed periods, and losing weight might not necessarily have any effect on your amenorrhea, because the PCOS doesn't go away. I'm also fairly sure, if memory serves, that PCOS makes the body more resistant to losing weight. PCOS may make it so that your periods never come back without medication, and that sucks, but it's NOT a failure, or a sentence to a life of barren childlessness.

I do know several people that have gotten pregnant even with PCOS, and one or two that can't, and I do know that weight, in and of itself, has no bearing on whether or not someone can get pregnant. If your /doctor/ is presenting weight loss as the solution to your PCOS problems - well, that's your doctor. I'm just some schmuck on the internet. But I'd be awfully suspicious.

On the other hand, more exercise IS correlated with heavier periods, so that may be your key. And again, that's measurable, and something that you can succeed at - providing you're using things like increased endurance, increased repetitions, increased time, increased flexibility, etc. and not just whether your periods come back - in a measurable and non-arbitrary way.

I don't think it's hypocritical. You have medical reasons for wanting it; it's not because you think you can't be healthy or happy if you don't hit some number on the scale or fit in a certain size pants.

As for the PCOS, I echo what Bah_bug said. I have it myself, & the ob/gyn who diagnosed me almost did cartwheels just to hear I was able to lose 6lbs because she said it was so difficult for PCOS'ers to lose. She described it as your body thinking it's pregnant & wanting to hoard weight. It took years for someone to diagnose why I wasn't having periods, & had gained so much weight, though I blamed myself for that. The doctors I was seeing did too though, so no one bothered to look beyond me being fat. It took me years to find someone who cared enough to listen to the fact I only weighed 125lbs when it started. At 5' 4" No one could say I was overweight, especially since 10lbs of that was probably boobs & back in high school a good part of that would have also been my perm.

I discussed the fertility issue with my current ob/gyn last year, & he never suggested I lose weight, although when I brought it up he said that could help. It's nice to have a doctor who listens to me & takes my problems seriously without just seeing the fat & not feeling the need to look any further.