Given there has been no further discussion here, I'm going to assume there is no active development on this issue. I manage a software development team, so I know all about development priorities and timelines. However, I think Evernote is running the risk of releasing half-baked features just for the marketing splash and not delivering on basic functionality. I have been a Premium user for years and have seen this in various forms across the platform.
If you offer annotations to PDF's baked into the client, you need to offer basic features like resizing stamps. It's OK to end up with this as a missed requirement. It's not OK to not address it at all for more than two years after it was noted and reported. I happen to agree with Evernote's direction of phasing out products like Clearly, Hello, and Skitch (ironic, on this one though) so they can focus on core experience. Well, it's time to focus on this core experience - get your annotation engine up to snuff please.