PAD's original v1 X-Factor was good. It was basically an X-Men comic with a sense of humor. But his v3 X-Factor is a whole other beast, especially in this first collection. The humor and characters are better than ever, but beyond that the whole premise shines with its focus on a detective agency rather than typical supes.
Beyond that, the first X-Factor was somewhat dragged down by its crossovers. PAD dealt with them well, but they dragged down his storyline, particularly the X-Patriots, who were around forever while X-Factor was cross-overing. Here instead we get X-Factor as the heart of the M-Day mystery, then when we do get crossovers, PAD makes great use of them, such as when he sends Layla to a future. (Layla, by the by, under PAD is one of the characters in comics, and it's a crime that she hasn't been used in more recent years.)
Finally, we get X-Factor #39, which is one of the most traumatic issues ever in comics. Wow.
Some characters have good continuations from the original volume here (mostly Strong Guy, as Madrox never got enough attention in v1 and Rahne gets moved off to another comic before she gets a chance to shine here). But this can be read entirely independently, and if you only read one PAD X-Factor omnibus, it should be this one.