Mediasoup has a bit more modern codebase and offers a rather low-level framework to build your own SFU. Whereas Jitsi videobridge is more of a ready-to-go SFU, but less flexible.
Mediasoup has very good node bindings, which may or may not be an advantage to you.
They offer similar (good) performance, although Mediasoup has a slight edge here. They're both very actively being kept up to date with the latest standards (in contrast with Kurento which is now as good as dead after Twilio bought the team). This is very important since both the spec and browser implementations are a fast moving target.
Disadvantage of mediasoup is that it is mainly maintained by just 1 or 2 persons and not yet used as much as Jitsi, so it's a bit of a gamble to start building your product on top of that.