For starters, you are using QuickTime to record the screen at 2560x1600 pixels in real time. That alone uses a lot of CPU and GPU power taking it away from the rest of the system. This will amplify any lag that you will have.
For a fair comparison, but not as sharp of course, you can try recording with an actual camera.
I have a very similar model (Late 2013 2.4GHz/8GB/256GB) with the same GPU and yes, there is some lag entering Mission Control for the first time, and using apps like iMovie, Aperture, FCP, etc. But once it's up and running it's not bad at all. Mostly an initial clock up from idle.
But a lot of it is that it's running at such a high resolution off integrated graphics, I agree. For example, when I plug in my 1080p monitor and use it exclusively in clamshell mode, it's smooth as butter 100% of the time. But when I open the MacBook and use it's internal display it will stutter from time to time. A lot of it is OS X using lots of effects for windows/transparency.
I do think it will improve over time with later software updates, and hardware down the line of course. But for now, I don't think it is unbearable, and if it is, choose a different laptop, easy fix.
Personally I'd rather have a nice high resolution screen to do my work on with slight lag here and there than something like a MacBook Air LCD, lower resolution and quality, but smoother. And this is a 13" highly portable laptop. If you want the best experience possible, go with the 15". But there are tradeoffs for portability and a lower price.
I do agree that the lag is there though, I've had mine for around 5 months now. And I see it, but hardly care to take notice anymore. Some people just get bugged by it more. Anyone ever play GTA IV on a PS3? That is some lag
As far as actual GPU power goes though, this thing runs most anything I throw at it. Games like Portal 2, Call of Duty, Need for Speed etc. all run just fine. It even plays back 4K video from my Moto X without stuttering a bit. So it's plenty powerful, it just has some lag with animations.