i had to put a sd hotrails tele bridge pickup in that black tele i finished last month. Compared to the Sd jazz in the neck it was lifeless and dull and i recommended the guy changed as soon as he could!! the neck pickup sounded great so i know it wasnt the guitar i built making it dull
I think people who buy these mini or stacked pickups dont quite realise how much the physical size of a pickup determines its tone.
for a start you have the issue of how much of the string the pickup 'sees'. A full size humbucker is literally looking at more string than a mini humbucker.... i feel this counts for a lot - especially with bridge pickups where the tone can be quite poor if too close to the bridge. the string just moves less in that position.
the actual dimensions on the coil are important as well - tall thin coils sound different to wide flat ones. compare p-90's, jazzmaster p-ups and fender black doves to fenders usual single coils.
Obviously this all works together with stuff like number of windings, wire and magnet type and all other elements of construction. thats why i like to have Tim making the pickups, rather than continue to use the ones i have made myself ( although i did get some nice sounding ones it was more fluke than skill!!!)