We're making a better world... All of them better worlds.

Nope, pushing on a person's chest the proper way or shocking them with the proper amount and force of electricity can bring people back from the dead. I bet that if science wasn't so confined by morality we could do all sorts of neat things that "Magic" accomplishes in fantasy settings. I'm not advocating the destruction of morality, but I do believe that through science eventually we as a species will be able to do just about anything.

if the gods do not pay attention/don't care, then you have to come up
with an alternate explanation for devine magic, or get rid of it.

Core 3.5 already has a great explanation for why clerics without a
patron deity get spells. I prefer to think of it as the picnic theory.
You don't really care if ants are taking away your crumbs at a picnic
and really until a cleric becomes very powerful that's all he's doing.
It doesn't tax deities to have clerics wielding divine power.

I am of the opinion that, as GM, you are only to place things in a
world that effect the PCs, if it doesn't effect them, why does it
exist?

I believe that as a GM my job is to create a world that's realistic enough for my players to suspend disbelief. Fantasy settings tend to have real definable gods, and I have no problem with that. Just because a PC doesn't interact with a deity doesn't mean he won't interact with said deities church or followers. Having something, even something that just sits there, gives me more options as a GM than not having something in the world. People worship things in our world they can't even prove exist. If deities are a proven thing then of course they'd be worshiped.

Eventually PC's do have the potential to get to the point where they are recognized by even the gods. Isn't that more of a reward than having a deity hold your hand the entire time you've been adventuring? What good are rewards if they aren't earned?

As for the gods messing around with meta-humanity and such, it depends on whether or not they draw power and/or strength from the beings who worship them. If that is the case, then stifiling the power of a rival by killing said rival's worshipers would be in one's interest, and the gods would care about the acts done by mortals in their name.

The Ori at the end of the Stargate SG1 series had a lot of involvement, but also drew strength from the sheer number of worshipers. The Ascended, almost virtually the same and not drawing power on the 'lower planes' like the Ori, actually had a policy of non-interference (though this was broke on occasion, with dire consiquences).

In older D&D settings, the astral plane had many bodies of dead gods who had no worshipers and effectively had died. The githzari/githyank (can't remember which) had their entire nation built on one such god corpse.

Of course, if the gods don't draw power on their worshipers, and really don't care what mortals do in their name, they can still come down to the 'lower planes' from time to time out of sheer boredom. Like Zeus and Ares of the Greek pantheon (though probably for more than just a nookie).

Then again, if the gods themselves just exist and don't bother with mortals, divine magic can still work. Just like ork technology in WH40K does, divine magic can work just because the priest believes it does, and therefore, it does.

Anyhow our conversation is very much off topic, and I'd like to wrangle it back in. I'd really like input or even written up deities from you guys if possible. We could most likely start a whole different thread for discussing world building theory.