How hard is it to include all music from a game or a series of games? Seriously. Unless it's something like the muted music in Super Mario Brothers 2 (during the pause screen), I don't think expecting all music is out of the question. Frankly, I think it gives people all the more reason to say screw the hard release and resort to downloading what they want off it...Why pay for an inferior product?
Which also leads me into a second argument, I'd guess mostly the same people here in this thread complaining about the box sets being incomplete are the same people who complain about the lack of track looping on soundtracks. I've never really understood that complaint either. Would you like them to double the amount of cds produced just to loop tracks twice? I don't see the incentive there. What's the point? I think I have even heard people complaining about that new Motoi soundtrack and how it didn't loop (EoE I think?). You want them to take a 5 cd soundtrack and loop the tracks on it, effectively making it 10 cds? Seriously? I'll never understand that argument.
Back when Star Ocean: Second Story and Valkyrie Profile were Sakuraba's defining works (at least to incoming fans), I believed looping tracks would have helped the releases a lot. Over the past 5 years or so, I think I've seen this argument largely disappear...It doesn't come up nearly as often as it used to and the usual culprits are the ones that have always been singled out (Seiken 2, FFIV, SO2, VP1, SOTN and Wild Arms 2).