It's not really an issue with ZFS itself. It's a great filesystem. GPL isn't the only way to do open source. It's the way Linux has chosen and that has pros and cons. Not integrating so well with other open source licenses is one of the cons.
That depends on what you want. If you want a license that will play well with closed source software, then yeah, it's a downside. But the GPL family comes from the perspective of a developer who wants to retain their rights while respecting others' desire for the same. If you care about your rights, then this is an upside.
>"It has a weak per-file copyleft (like version 1 of the Mozilla Public License)"
The CDDL isn't a strong copyleft licence. It doesn't give a shit what larger project you include the code into, and it doesn't give a shit how you licence the resulting binary. It's considerably more permissive than the GPL.
The conflict is entirely on the GPL side.