Here is a summary:
1) Shaman specs outside of Restoration lack survivability.
2) No pushback resistance for Lightning Spells put a hamper on solo grinding / farming as well as in PvP.
3) Totems immobility and short range need to be buffed.
4) Other classes got new skills/spells in TBC that changed their playstyle, Shamans did not.
5) Enhancement shaman lack significant ranged combat abilities as well a way to chase down fleeing opponents.
6) Threat management is a bigger issue than ever with the TBC talents boosting shaman dps.
7) Shaman have issues handling an assist train. (When someone gets zerged by multiple opponents).
8) Lack of a way to deal with other classes' crowd control abilities put shaman at a distinct disadvantage in PvP.
9) Off-spec Shaman itemization is poor in Karazhan and beyond.
10) Flametongue and Frostbrand Weapon both scale poorly.
11) Windfury and Stormstrike demand the shaman using the slowest weapon for maximum dps gain, but that concept is counter to the weapon normalization introduced in patch 1.8.
12) Shamans need more control over their fire-and-forget Totems to direct them at a specific target or to stop them from breaking cc.
13) The large global cool down associated with dropping four Totems in combat makes it difficult for the Shaman to be responsive to changes in combat.
Read the whole list through the link. If I've misinterpreted something, list it below.