In Cata and other areas where you would complete a quest and get armor with multiple choices as to what armor to choose. For example, there was a quest where when it finished, it checked the choices, and chose a piece of armor my character couldn't even use, which was cloth, but I have a Prot. Paladin, and passed up Male armor with 100+ Boosts to the armor, like 80 Stamina increase, 120 Dodge increase, etc. Since I wasn't geared for Cata, but instead, the bot chose some Cloth... I think this should really be looked into. Even though I can wear Mail, but Plate is recommended, the better armor should be chosen.
In MoP, it should only be giving you choices based on your class and spec. For example, As a prot paladin, you should be given a choice of plate armor with dodge/parry/ect and a dps plate armor. I cant remember if this is only for MoP quests though.