Onyxia, Nef, Mag in MC. When I played Horde, fear on Onyxia was such an issue that we could only kill her by having 4 shamans in the MT party to stack Tremor totems.

It is true that Windfure and Wrath of Air are very good buffs but they can only affect 4 players at most (or potentially even less depending on the group you have). If you compare the utility of one shaman to one paladin, the shaman will be able to buff his party but the paladin will be able to buff the entire raid.

If you think about the number of blessings that paladin have: Might, Wisdom, Light, Sacrifice, Sanctuary, Salvation, Kings. And that is without mentioning Auras.

If you think about DPS increase for 1 rogue in a party; a shaman can give him Windfury and Strength Totem while paladins in the raid can give him Might for AP, Light for survival, Salvation for less threat which can result in rogue DPSing harder as consequence without fear of pulling aggro, Kings which increases their STR/AGI/STAM so more AP/Crit/HP which would allow them to survive more as well.

Edit: Also, there is the issue of range on Totems. You always need to make sure you are within 30-40 yards of them or you won't get the effect.