Where are you getting these damages numbers from? Seeing as they are in the 4 millions, I'd assume you've been keeping a damage meter running the whole time, which is ok, but won't necesarily provide the most accurate picture of how an individual's damage contributes. If, for example, you are killing normal mobs in your daily adventures, and the mobs are dying 1 second before your mages get their last fireball off, or if that last fireball crits buts kills the mob before it can take ignite damage, you are going to see a reduction in their over all damage in the long run, even though in extended cisrcumstances they may perform just as well as any other DPS. It doesn't help that moonkins tend to spam wrath, which has a short cast time that may provide the illusion it is beating out the dps with the longer cast times, but only because the moonkin gets that one extra wrath in.

As far as killing trash and non-elites goes, I would say that a better estimate of performance would be group DPS, and for extended fights such as bosses, total damage done and individual DPS is what you want to look at.

Bottom line though, I would say you should go beat up a targeting dummy with a fresh damage meter and look at those numbers to determine if your characters are up to snuff.