There was also the rest of the Web of Spider-Man series that ran during that era--#8-12 (originally collected as Spider-Man: The Extremist would pad out another Complete Collection nicely. 19 issues would make up a good Complete Collection, plus any of the Web of Spider-Man backup stories that weren't covered in the Gauntlet Complete Collections.
As for Omnibuses of Dan Slott's Spider-Man run, it seems so obvious that I'm surprised they haven't happened already. I'm especially surprised that Slott's Tony Stark: Iron Man got an omnibus first. Or that we didn't get a Superior Spider-Man omnibus when the second Superior series came out. Not to mention that if I remember correctly, the Slott-era OHCs only started during the Superior-era---the only OHC released of the 'Big Time era' was Spider-Island, so an omnibus would be especially welcome.