The major difference between the Horde and Alliance is Shamans vs Paladins, Shamans are naturally a little better in the process of getting the flag from one end of the field to the other. Whether the shaman is actually the flag runner or not, he is very good at slowing down allies chasing the flag bearer (Earthbind Totem, Frost Shock) and a decent flag runner in his own right (can slow down the allies and can increase his speed with Ghost Wolf.) Paladins can be good flag runners, I just don't see it as often.
In lower level WSGs, twinks are much more powerful than in later BGs, because the enchants that are on some of these 29 characters are the same ones that level 60 characters have (ie Crusader, Lifestealing, Health, Agility, etc.) Those kind of enchants boost the offensive powers of players more than Defensive powers, so an offensive class like a Shaman could be twinked out to be more effective than a defensive based class like a paladin even if they have the same enchants.
The levels in your BGs may also be a factor, try looking at the average alliance level vs the average horde level (while I think its stupid to join a BG when you are lower than the level 8 of the given bracket, some people feel its fine to go in at the lowest level possible,) if there is a level gap, that can make a huge impact on the outcome. Also look to see how many Horde have high end enchants compared to the Allies, if your group is filled with twinks and theirs isn't, then its a no-brainer that your group is stacked and they are out of their league.