Every other program shows the tax PDF forms as empty yellow pages. It's by design.
I assume it has something to do with being a "smart PDF" which generates scannable QR-like codes based on the numbers entered.
It handles most things you need for a pdf that you can do in reader.
I've encountered PDF's that simply don't work in Preview by design -- as far as I've been able to figure out, Preview won't run JavaScript embedded in PDF's for instance.
But all my experiences with filling out forms, makring up annotations, and all that jazz has been totally on par with Acrobat Reader. The same tools are present and all seem to work generally the same way.
What specifically have you run into that is poor in Preview?
I fill out forms in encrypted PDFs all the time with Preview, never had a problem.