What other B-sides could they have put on? Sure, they could have put on some rare stuff like "I'm Not Your Baby", but that stuff was few and far between.
As I recall, in terms of non-remix material on the B side disc they had:
Summer Rain
North and South
Happiness is a Warm Gun
Salome (represented via a remix)
LWTSG (represented via a superior remix)
I guess they could have done a CD of just B-sides. That would have been:
Korova 1
LWTSH (original)
Night and Day
Salome (original)
Where Did It All Go Wrong?
Satellite of Love
Paint It Black
Fortunate Son
Viva Davidoff
Slow Dancing (original)
Holy Joe (guilty mix)
Holy Joe (garage mix)
North and South of the River
I'm Not Your Baby
Happiness is a Warm Gun
Two Shots of Happy
Slow Dancing (full band)
Stateless
Summer Rain
Always
Big Girls Are Best
That's a 21 song CD though, and while the B sides that were produced for the first best-of would have been album tracks for any other band, I'm not sure the band's B side output in the 90s was up to that same par. A lot of the songs on this list are either covers or demos, and while there were a few demos/covers in the 80s compilation too, most of those songs were fully produced, quality tracks. This bunch, not so much...
Not to say that the remixes were any better, but given where the band's head was at in the 90s, remixes might have felt like a closer representation of what the band was up to!