Well, the first thing you can do is stop sending PDF to your conversion house. That is the most crappy format to start from...
With regards to your image problem, that is just the current situation. Downsampling is really depending on the algorithms and for a lot of readers they are not great. Also, high resolution is fine, but there are millions of readers that do not support those resolutions. So, there is a problem there. Some publishers make two versions. One with a high resolution and one with a lower one. If you have full screen images, you could use a SVG wrapper. Downscaling of those are usually acceptable.
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