AndyWatson
I have almost the identical scenario to you. My first game was done with eclipse, phonegap and the admob plugin. Life is good there. Fill rate is good and the payout is nice.
My next 2 games I went with Concoon/mopub and I had a very similar problem to you. Low fill rates, ect. Basically what I did was turn off the Marketplace for those apps. I personally don't think the marketplace is worth it.
So for my Droid apps, I only have the admob network running and it's around 88.8 percent fill for the last 14 days.
My iOS apps I just have iAds working. Those fill rates are around 78% for the last 14 days.
I am really hoping phonegap implements some kind of direct canvas because I love having the build control of using eclipse and xcode for my final builds.