The 2012 retina macbooks include an HDMI port (in addition to mini displayport)... I assume the 2013 ones do too.
Most projectors i've encountered recently only had VGA, with a small handful using HDMI. Chances are you will need adapters most of the time anyway, unless you want a laptop with lots of ports on it.. In that respect, mini displayport is good because the connector is small and doesnt take up too much space, and is easily adapted to several other formats.
How many people are regularly flashing firmware on network devices or configuring access points? These are niche requirements, the vast majority of apple customers will never be doing such things. And for a device like the macbook air, the case isn't even thick enough to put an ethernet or dvi socket on it...
I've encountered situations where someone with a non apple laptop was unable to connect to a projector too, for exactly the same reason. In fact, there's some laptops these days which don't include any video out capability whatsoever.