I actually agree with OP sadly! I just bought the rMBP 13", and I know it doesn't have an i7 or anything but the OS should not lag like this! Literally everything with a UI animation lags basically, it's depressing. I run W10 on my main desktop which only has an i5-2400S (and an SSD) in it and it's blazingly smooth. I love Yosemite's look and feel but the skipped frames really bug me this shouldn't happen with a modern computer fresh out of the box. I run my retina display at 1440x900 and occasionally 1680x1050 (use Retina Display Manager to switch on the fly) and they both lag. Not only do those resolutions lag but 1280x800 sees some occasional frame drop as well. This is with reduced transparency disabled of course, so as the OS was intended to run.
The things I most notice drop frames is NC (always), while scrolling at top or bottom of Finder when things are displayed as icons (happens in Desktop & Screen Saver as well with the pictures). The button to return to System Preferences has dropped frames when clicked, resizing Safari (kinda ok with this one but it's horrible when watching a video like YouTube), the green button (maximize?) occasionally, the gesture based things (Launchpad, the double screen view thing, etc) skips some. I know it may seem like I'm nit-picking but it's just something I wouldn't expect to happen on a new computer, yes if it was a few years old though I could understand.
Is there anything I can do to fix this other than turning on reduced transparency and whatnot? I've never really used prior OS X versions but watching and using the little I did it was always buttery-smooth until Yosemite. I feel they just have too much blur with the OS that isn't optimized well enough and they're just saving to fix it for El Capitan cause I've read that the lag is apparently fixed in El Cap but I haven't tested it. I might try dual-booting El Cap and testing it...