If your apps rely on some kind of package or custom modules that specifically rely on Express then it might be worth sticking to the older system.
However, if you’re working with green field apps with no prior constraints, I would recommend using Shopify’s latest framework. They purchased Remix a few years ago, so they’re committed to using it in their ecosystem.
You can still use your own framework, but then you’ll have to make sure you’re keeping up with the AppBridge/Extension compatibility changes.