Take this with a grain of salt as I've not been back into WoW for very long.
I'd focus on making sure the debuffs and buffs complemented each other. So, group 1 (physical dps) = druid tank, warrior, rogue, hunter and probably use the resto shaman in this group. Second group (magic dps) would be DK tank, mage, lock, shadow priest and pally healer. I'd also do it this way to put all my melee DPS in one group to simplify IWT management and slightly easier-to-predict movement requirements. Might switch the resto sham and holy pally depending on how well they heal on the move and possibly to have the holy paladin doing things in melee range, which might help certain fights where you basically run all over the place.
Also, 5.0 will probably shake things up enough to require a refactoring of synergy.
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