Off the top of my head, there are a number of tracks that were given commercial release that don't appear to have made it. The biggest omission, to me, is She's Not There.
Also missing are the extended versions of Don't Dream It's Over and World Where You Live, the 1996 remix of the former, the US-only mix of Distant Sun and the Alternative Mix of Instinct.
Beyond that, it's hard to know what we're missing because we don't know what's in the archives. I had hoped to hear the following:
Demos or studio takes of the two songs that were merged to form Fall At Your Feet. It appears that an early version of the song is to be included and it's possible that we'll discover that the other portion is contained in another as-yet-unidentified track we're about to get, so I haven't lost all hope (anyone who's not familiar with The Same Language As Me will be in for a surprise...)
The slow arrangement of Locked Out. I'd have also liked to hear more outtakes or alternate mixes of material from Together Alone: Chris Bourke made mention that Bob Clearmountain left out a lot of sounds the band recorded in order to create less cluttered mixes. I suspect he made the right call, but I'd have loved a "kitchen sink mix".
There are many songs that CH played live that we assumed had been, at least, demoed either by Neil alone or the band in rehearsal. Frank's Dark Past, for example, seems so well-formed and well-known to the band that it's hard to think they just made it up on the spot.
I'm also a little disappointed that the most interesting demos from Neil and Tim's Woodface demo sessions didn't make the cut, presumably because they didn't end up being CH songs. They were first issued on Finn Bros singles (suggesting that they were being considered as Finn Bros recordings) before some of them made it onto a previous Woodface reissue. The fact that the number of songs from those sessions included on Woodface has now been increased is welcomed but the omission of the most interesting ones of the bunch - Prodigal Son, In Love WIth It All and Strangeness and Charm - is unfortunate.