A quick glance shows a couple of things:
* Automatic cluster scaling, so your PaaS deployment is as small as possible. Cloud Foundry doesn't have this, and I wish it did
* Flynn has built-in service discovery, in Cloud Foundry you bring your own (if you want)
* Flynn comes bundled with some data services
* Flynn has no BOSH equivalent, so there's nothing there to bring back VMs when they fail, perform rolling upgrades or manage the IaaS
* Flynn doesn't seem to offer a metrics stream, only logs
* Flynn builds apps from source, so not sure how that works for compiled Java/Go, or anything you'd run with a binary buildpack
* I couldn't find anything about role-based access control in Flynn, something Cloud Foundry has (which can be backed by LDAP for enterprises)
* Flynn only appears to route HTTP traffic, so no TCP routing for IoT workloads
* Cloud Foundry is run at massive scale in production for mission-critical workloads by banks, payment processors, IoT data ingesters, manufacturing companies, research companies, governments and everything inbetween. I can't see any evidence of the same being said for Flynn.
* Flynn is owned by one company, Cloud Foundry is owned by a non-profit organisation affiliated with the Linux Foundation and can never be transferred back to a regular company. This prevents the sort of nonsense you've seen in the Docker community recently.