Hi Lars Øyvind and Tobias.
I have upgraded both an R1 SP2 and an R1 SP3 site to R2 with the manager option "Upgrade Site from 5.1 SP2", and both worked fine.
SP3 only contains 21 bug fixes so its a much smaller release than SP2 that had 122 bug fixes. One of the bug fixes in SP3 related to enterprise sites required a change in how the configuration loaded causing incompatibilites with some modules.
You can upgrade to R2 from both SP2 and SP3, the upgrade text should have said that.