Everyone has his favorites. Mine are:
Wedding Dance
(+) a good story, fleshed out with new quests. Interesting equipment, including some sexy armor. OK kingdom management.
(-) very easy, and the middle game becomes a bit boring, while you are taking over the map to see the grand finale.
Sword of Damocles
(+) a challenging endgame, unequalled kingdom management, unique troops, great new civilisations
(-) the midgame is a bit boring, as the player troops overwhelm the native civilizations
Prophecy of Pendor
(+) Very challenging enemies, fleshed out civilizations, a number of unique mechanics: knight orders, weapon crafting.
(-) no weaknesses to speak of, but lacks the quests of Wedding Dance, and the kingdom management of Sword of Damocles.
The Eagle and the Radiant Throne
(+) guns and gunners done right, and fitting well amongst the other units. Very detailed civilizations, great ambiance.
(-) again, no weaknesses, but less new stuff than the above mods.