For me, it comes down to 2 issues:
1) There aren't enough choices available to all divines, regardless of race.
2) Why shouldn't I just use a two-hander?
The first issue is simple, and has a simple solution. There are 5 faiths available (except to FR iconics), and 3 of them are only available to one race each. Not only that, each race that has it's own favored weapon, along with enhancements to buff that weapon. I've seen more than a few twf melee favored souls, but they were almost always elves or drow. Everybody else except warforged miss out. I would suggest to the devs that they make more faiths. The Sovereign Host is a pantheon, after all....
The second issue is a bit more complex. You see, it's not hard for anyone who doesn't like their favored weapon choices to find ways to *completely ignore* the entire idea of favored weapons in favor of picking up a two-handed weapon. If you're a half-elf you can take fighter dillie. For humans and everyone else you can take a fighter level or even use up a feat slot. 2-hand weapons use 1.5x your character's strength modifier for damage. Add that, along with the large number of stacking strength bonuses, then compare it to what you get from wielding a favored weapon. All the feats and enhancements that benefit favored weapons are to-hit and damage bonuses. One might think that the lack of to-hit bonuses would hurt a melee divine... however, to-hit bonuses are the most common buff in DDO, hands-down, and most of them stack. To solve this issue, favored weapon feats and enhancements should give something that a two-handed weapon does not, such a doublestrike/doubleshot, spellpower, or enhanced critical profile.