I'd say the serve was the biggest one.
I'd actually say the backhand and the return of the serve were Nadal's big problems. I've NEVER seen Nadal return Fed's serve so poorly in any match of their rivalry stretching 15 years. And of course Fed's serve was not any better than it usually is (more on the contrary actually). Furthermore Rafa's backhand was also AWOL. Nadal completely lose the confidence in that shot. So he could only play is safe away from the corners or run around it. Hardly any flat DTL backhands or cross court winners - so basically he lost control as soon as his backhand was attacked. Which is strange because he hit the backhand great in RG and in prior rounds in Wimbledon.
Overall, Nadal lacked belief. There is a reason he is 0-14 against Fed and Djoker in last 14 Non-clay matches. As I had said before, in all the pre-SF matches in Wimbledon, he broke early and won set 1. I always wondered what would happen when he plays from behind and loses set 1. Same thing in AO 2019, when he was playing amazing - until the final where he was behind early and lost all confidence.
Problem for Rafa is that he is naturally aggressive ONLY when he is in the lead (breaks early or leads by a set) OR he is about to lose the match. That cost him dearly against Fed, as he unexpectedly played his worst match of the tournament by far. I was very surprised because I've not seen Nadal under perform like this on the big stage. But then it happened in AO 2019, now in Wimbledon - even when he played great against dangerous opponents such as Kygrios and Querrey in prior rounds.
All that suggests is that when push comes to shove, Nadal doesn't have the belief against his biggest rivals (Fed/Novak) away from clay. The one sided (0-14) h2h highlights that..