Most people don't really carry around Ender Chests since you can't break the Ender Chest to get it back without Silk Touch, but many people do carry around PCs since it is convenient to be able to change up the party at any time. Furthermore, Ender Chests are not usually found lying around, whereas all Pokemon Centers have PCs as of version 9.0.0.
I would like to state though that the Item Storage System hasn't been a thing since Pokemon Emerald, so might be considered an outdated feature. I personally have never played a Pokemon game where the PC had the Item Storage system, despite having played Pokemon games since I was a kid. Still, it would be a nice thing to add.