I recently re-read the TMP book, but am blanking on what aspects cannot be reconciled with later screen canon. Can you elaborate?
Well, there's never been any elaboration on the idea of a fast-spreading "New Human" movement that's somehow developed collective consciousness and superior intelligence, or the notion that Starfleet personnel represented "primitive" throwbacks from that evolutionary process. And the idea that high-ranking Starfleet officers have communications implants in their brains is hard to reconcile with anything we've seen since. Not to mention that the novelization shows perfect holographic communication in use a century before DS9 introduced holocommunicators as a prototype technology. Also, I doubt that the Straits of Gibraltar have been dammed and the Mediterranean reduced to a small lake in the canonical Trek universe; I'm sure there have been plenty of shots of Earth from space where the Mediterranean Sea was still visible. And that's all just in the first 30 pages.