EDITED: They used Unity for Pokémon Brilliant Diamond & Shining Pearl. I'm not sure why they switched back to in-house for Arceus and these newer ones.
The main issue seems to be their release schedule as well as their inexperience with games of this scope, and likely not the engine itself (although it's likely a contributing factor).
Digital Foundry put out a good video showcasing how the game performs and comparison to Arceus https://www.youtube.com/watch?v=pBZqt7D24Zc Honestly, Arceus which was already rather ugly compared to Breath of the Wild and certain other 3rd party titles on the Switch, is a much better looking and detailed game then this new generation.