i don't see why you're making imaginary matchups... it's totally unnecessary IMO.
shaq/kobe was not all that great of a duo. shaq was awesome of course, and kobe was very good but at that time was a total headcase. it was more shaq/phil jackson that won those three championships, not shaq/kobe.
kobe seems to be smarter and a much better team player now, but shaq has been gone for years.
shaq/wade - as good as shaq/kobe, and that's with an aging shaq. throw in your referee conspiracy theories if you like, but the results are there.
duncan/ginobli or duncan/robinson - dominant where it counts, and they have the hardware to prove it.
nash/stoudemire - no hardware yet, but a fearsome duo.
yao/mcgrady - if yao keeps improving like this and mcgrady can turn a miracle by staying healthy, they will be as good or better than shaq/kobe were. might even be there right now.
anthony/iverson - just kidding.