I'm voting for this to be a software problem as well. The retina MacBook is packed with a very powerful GPU - I think it should handle this amount of pixels.
But most importantly - it seems like there is too much variation from app to app - suggesting the coding has a great impact on the fluidness and lagging. Take iPhoto for instance, which is a somehow heavy app, but still runs smooth as butter. iTunes and Safari on the other hand, runs sub-par FPS on many occasions. When iPhoto can scrobble thorugh my entire photo library at 30 fps, I see no reason why Safari shouldn't scroll
http://www.aftenposten.no at a decent fps.
To quote what another forum member said about the case earlier:
There is no problem with the GPU itself, it's fine. It's an issue in OS X and the immature scaling system they're using is just not fast enough, it's still demanding too much from CPU/GPUs at the moment (the hardware is capable but the code itself isn't optimized for those hardware).
This is the first time Apple has enabled such scaling system in OS X with a Retina display, so there'll be issues and it'll take several months to optimize it.
They're already improving in each software update with better drivers.
If you can wait to get the rMBP next year and you're happy with your current system, then wait it out. It'll be much stable next year with further improvements to both the rMBP but most importantly, an optimized OS for the Retina displays.
Also, I'm seeing great improvements on the facebook news feed after resetting the entire Safari app, deleting cookies, autofills etc etc etc. This also indicates bad coding.
I'm not a pro though, so feel free to tell me where I'm wrong.