An extra 32 colour registers would have taken up a lot of space on the silicon... you forget that CSG's fabs were VERY old by the time the EHB was added.
I dunno, EHB uses a 6th bit plane and so would a true 64 colour system. Dual Playfield mode also used 6 bit planes too.
I don't think the palette of EHB is an issue given todays excellent image processing tools on PC and Mac to find a very nice compromise. But isn't EHB a severe slouch on the OCS/ECS chipset, hence limiting what kind of 25/50 fps (30/60 NTSC) games you could write anyway though?