This isn't as big a deal as it seems. Google haven't updated their AOSP Dialer app in years, and custom ROMs have been using their own forks for nearly as long. Furthermore, the ROM devs have been pushing their key improvements to the upstream main repository, only to be rejected. So this ultimately affects manufacturers more than users - the manufacturers either have to make their own Dialer or pay Google for theirs. Or they could potentially use an open source one from the ROM community.
The Messaging app is even less of a concern, given that a core feature of Android is the ability to install 3rd party apps for this (which often have better functionality).