Is there a reason why so many third-parties refuse to offer upgrades? Is it a complicated process? Is it easier to do on PS5/Xbox Whatever?
There are several possibilities:
1. Nintendo is discouraging upgrade paths and save transfers compared to the likes of Sony & Microsoft.
2. Sony & Microsoft are providing incentives behind the scenes for companies to offer those upgrade paths and save transfers, but Nintendo does not.
3. 3rd parties (but especially Square Enix) are choosing to combat recent economic downturns by pulling up the drawbridge and removing any costly QoL incentives for users to cut costs and maximize returns. Nintendo owners aren't exactly known for buying 3rd party games as it is.
There's probably more, but the most likely reason is some combination of 2 & 3. With how quickly Sony is burning every bridge they can find lately, I wouldn't be surprised if we stop seeing upgrade paths/perks with games on their consoles as well.