The lack of equally high standard replacements for software such as
For me, it's Devonthink Pro (http://www.devontechnologies.com/solutions/writers.html) in particular and also Lightroom. Yes, there is progress on Dark Table, but there's too much useful software on OS X and despite Apple's faults its laptop hardware still leads the pack.
Yes, the lack of ports on the new MBP is annoying. If I had to buy a new MBP today I'd just get the last version—which is still fantastic—refurbished, and kick the hardware can down the road a couple years.