If you've never purchased BR before on Blu-ray, as seems to be your case, the new set is the one to go for.
If you have the 5-disc Blu-ray from 2007, you should probably skip the new set. The photo galleries that were originally cut have been restored to the extra features, BUT Dangerous Days is still in standard def, not to mention there are a few other omissions here and there.
Basically, I consider the 5-disc set to be the Alien Quadrilogy (2003): It's great, it's got LOTS of awesome special features, and Charles de Lauzikira and his team should be proud of their work...but it could be even more awesome, like the Alien Anthology (2010).