There were some definite compatibility issues we ran into and while jQuery 2 isn't perfect, it's pretty good, good enough we felt confident switching back from Zepto. Nothing against Zepto, just pragmatism.
There's a media query available (with prefixes, right now) for pixel density – a retina MBP reports it as 2 whereas a standard one reports it as 1. So you can have a media query for a pixel density >= 2, etc.
Checking network speed is actually a great idea - we'll investigate this. The reason we use the img src (which as you noted means you might load two images) is twofold: so that if your image is the same aspect ratio, you'll get an immediate load of something before the better image comes in (without which you'll have a really nasty reflow). This also guarantees you'll get something that works if JS is disabled or unavailable.
Please submit pull requests or issues for ways we can make this better, we're all ears.
Couple differences: Skeleton was designed as more of a boilerplate than a full framework, and Skeleton focuses on being responsive through breakpoints (specific sizes at which the layout shifts) rather than a percentage-based grid system.