They do amazing work integrating CGI into live-action footage. Everytime th eimage is only CGI like in the starship shots, it looks like crap. I'm not sure if the behind-the scenes problem of the first season are to blame, or the art direction, but it just doesn't look realistic. Then again, I think Pixomondo often has the problem of looking "too much" CGI, even in their big budget work - for example the Kronos chase in "Into Darkness" looked at no time "real". But the touch-ups (changing the sky over the Jordan desert, adding two more arms to the alien) are genuinely great.
Another thing to notice is that almost all of the exemplary shots in this video are from the pilot two-parter - which is apparently where the show blew all their budget, as almost every space scene after that looked like real crap, and even in this video they had to use some heavy editing (zooms, fast-forwards etc.) to obfuscate the finished shots some time, because they simply didn't look as good.
That being said: Great video, and it really shows how much CGI actually went into the show, and how good most of it (especially in combination with live-action) actually is. Yes, the tMP model starships looked more realistic. But for everything else, a lot of it simply wouldn't have been possible without CGI.