Favored weapons are a lot like crossbows: Why would I use a crossbow when I can pick up a repeating crossbow and do 2-3 times as much damage?
You see, it's not difficult for any non-warforged divine to use up a feat slot, or take one level of any class with marital weapon proficiency, or roll up a half-elf FvS with fighter dillie, in order to gain access to two-handed weapons. I'm sure that even without doing any math, one can see that the difference between a longsword and a greatsword, for instance, is very significant. If you guys and gals want to make use of the favored weapon mechanic for divines, two things need to happen:
1) A greater variety of weapons need to be available as options. I'm sure you have all the pertinent information on favored weapons and faiths, and I am fairly certain that most of the favored weapons for the Eberron faiths exist in DDO already. It's not necessary to make any new 6th level faith capstones for all of the Sovereign Host deities, although that would be optimal.
2) The favored weapons need to be useful enough to the wielder so that deciding between the favored weapon (even the longsword) and using a two-handed weapon is a tough choice. I'm not saying that they need to deal comparable damage, but things like DR-breaking effects, ghost touch, doublestrike/doubleshot, increased critical profile, elemental damage on hit/crit/vorpal, or SOMETHING that makes the choice of weapons a tough one.