CPU performance isn't significantly better. Expansion ability isn't that much since it's just RAM and HD. HD are mechanical and wear out faster anyway. Not to mention slower. RAM can be expanded to 8GB and beyond but the controller handles 16GB (I think?). 16GB is overkill and you will be bottlenecked by other components before RAM becomes a factor in performance. For most people (maybe not you) 4GB of RAM is plenty. I routinely run Calendar, Mail, Safari (with multiple fullscreen windows with 10+ tabs EACH) and iTunes with zero slowdown due to RAM limitations or CPU performance. If I really need to, I can also run FCPX along with all of the above and it maybe gets a hiccup occasionally. That's more than enough for the average user (again, maybe not you). The MBP? The bottleneck there is the HD. Sure you can upgrade but most people don't upgrade their laptops (this is a sad but true fact), know how to upgrade components, don't care about it, don't want to care about it or some combination of the aforementioned.
A bigger battery doesn't directly translate to better battery life. MBP has a higher TDP CPU among other components that the MBA doesn't have. Battery performance will be the same between 13" MBA and 13" MBP. The 11" MBA will offer shorter battery life than the 13" MBP obviously.
The part in bold is simply your opinion (and mine for awhile) because some people don't need FireWire, Ethernet and DVD drives. For those people, having it doesn't simply mean it's a superior product. Superior is a highly subjective term. But for people who care about those ports and DVD drives (aka you) , then the MBP is superior no doubt.