The bezels on the rMB's screen are thinner and the lid is probably thinner so I assume there are tight space restrictions on the camera and the best they could do with those restrictions was 480p.
I don't see how they could add a 2nd USB port on the rMB or an SD card slot given the size and shape of the laptop. Maybe if they replaced the headphone jack with another USB port and bundled an adapter.
The MBA is actually thinner at the point where the camera is than the rMB. And while the bezels on the sides are thinner, the top bezel with the camera looks exactly the same size.
So yeah in 2012 they were able to engineer a 720p camera into a thinner space, while managing 480p years later in a thicker space.
It was disappointing.
It could turn out that 480p is fine-ish. Cameras are way more than just megapixels. Needs testing. But, there was no real hype or talk around the camera so I think it's safe to assume it's not very good.
Normally I wouldn't mind, it's just for videochat after all and it's not the end of the world that your boss can't discern every pore in your face. But it was disappointing in a more symbolic manner: Apple is willing to choose form over function in pursuit of this 'thinness craze' that many people are fed up with. It's a business decision that's not good for their customers.
Customers would benefit with a slightly thicker, slightly more capable device (e.g. more battery life) that will be competitive for 5 years. Apple benefits by reducing that 5-year buying cycle to say an average of 3 years, by focusing not building a device that stays fast for 5 years, but building one that's fast only for 3 years, and goes out of fashion quickly because their focus is on improving and tweaking the form, making everything outdated. It allows you to charge a lot more money for a pretty and fashionable design without spending on the best performing parts, and get people to pay you $1k+ every 3 years instead of every 5. It's a soft type of planned obsolescence that you can get away with, but that can receive backlash every now and then. Like a 480p camera in 2015.
Anyway about your second point, I think a 2nd usb port is definitely coming later this year. An SD card though... I kind of doubt it.
For one, SD cards have lost a lot of their importance. Internet connectivity is becoming so ubiquitous, and there are now over a dozen cloud storage services that give you 5-20gb of free storage. We're seeing entertainment turn to streaming (Netflix, Spotify). We're seeing cameras with wifi that can upload pictures to a printer, flickr or dropbox. So why do we still need an SD card? Sure it'd be nice, but it's probably a bit like the CD pretty soon. Everything is going wireless and to the cloud, storage and transmission of data no longer needs SD cards.
And secondly, it cuts into their products & revenue in two ways. One even the little space it requires needs space, needs parts, needs repairs, takes away from the minimalist design etc. And two, SD cards offer 20c a gigabyte storage. Apple charges (and gets away with it), $1.50 per gigabyte on its SSD drives. The Nifty devices are extremely popular and SD cards allow you to effectively get the 128gb base model and still get 256gb+ storage at a much cheaper rate. It's like Apple had a port that turned your i5 processor into an i7 but at half the price. No way they'd want to keep that around if they didn't have to.
So I've got my doubts. The rMB is definitely the device to fully usher in an era of wireless & cloud. (safe for the USB-C port for charging and video output, which are both still sub-par. Slow to charge for wireless charging, and no way to currently reliably do 5k throughput on wireless with near zero latency.) So an SD card is not an automatic choice, especially for future 2016-2020 generations.