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I have put down a lot of water based poly. I have never had it look terrible on the first coat. How are you spreading it? Maybe you are getting bubbles. BTW the water based poly with 5 -6 coats is holding up much better than the rooms we used oil based and applied 2-3 coats. The two part stuff we used int he kitchen did nto hold up well at all, but it got a ton of abuse (2 200 pound dogs, 5 kids and their followers, spills, etc).
That too me looks like a poor sanding job and/ or poor staining job and has nothing to do with the clear coat. Test a small area with a second coat of clear and see if it goes away.
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