Second season it a total disaster regarding The Goddess. Almost made me cry...
It seemed like script writer(s) was/were Fluttershy hater(s). Makes me want to put them in the proverbial SHED!!!
-- Edit --
Sometimes it seems to me that they realised that they have made a character too strong and capable, that in the moments of emergency she can easily render other 5 almost futile (even w/o various magic spells) and were kinda afraid of where that could lead. So they tried to sweep her under the carpet psychologically in the Second Season. Has Celestia be my witness, that always makes me explosively mad when I watch. Fortunately fiction has one good feature: when you make some characters, they start living on their own, mostly by the vector established by a few first strong impressions of them. If the character is strong and deep, you simply can't spoil or kill them later. So I know the truth, she is simply superior:
- she has The Stare;
- she can understand, care and tame anyone (up to wildest monstrosities like adult dragons);
- she can outfly even RD if absolutely necessary (season 2 ep 2);
- she can be assertive, still she is gentle, polite and kind towards everypony deserving;
- she's got the look;
- can cook and sew (at least with the help of adequate designs )
... I can probably list forever. Anyway...
And she really is!