I'm gonna offer my insight here, and maybe some of this has been said before as I didn't read through the entire thread.
Natural sounding drums do NOT have to mean a bad metal mix. Listen to As the Palaces Burn by Lamb of God. Granted, not everyone is going to be a fan of that style of mix when it comes to metal, but I for one like it as you can tell an ACTUAL band is playing, and it's still clear and concise.
I think the best approach is to get your Overheads sounding nice and clear and natural, and then to mix in your close mics just to taste. You can still use something like drumagog to do sample replacement, but use it to ENHANCE the sound of your snare, not to change it. I usually try to get my drum mixes to sound like Fredrik Nordstrom (old-school Arch Enemy, Colony/Clayman In Flames).
Kick - Do a sweep with a parametric EQ to find out where the attack of the beater hitting the head occurs. In my experience this is usually somewhere around 3.5k. Once you find that point, apply a high shelf. Then apply a wide cut to lower the 250 - 1.5k range. You can apply a slight (1 - 2 db) low shelf to your kicks if you want, but this is optional.
Snare - sounds fine to me actually.
Toms - more close mics. Maybe consider slapping drumagog on here and replace them with samples.
guitars - Way, way, way, way, WAY to freaking digital sounding. I don't like listening to these at all. I agree, a cranked tube amp is definitely the way to go, but you can get GREAT tones out of amp-sim software as well.
Typically, I record DI tracks of all my guitars, 2 per side which makes 4 total takes. Then I run each take through 3 different instances of Peavey Revalver. (which means I have 12 total guitar tracks in my mixes) If you experiment and have an ear for good tone, you can create really heavy, full, and most of all organic sounding guitar tones just from sims.
If you have to work with these guitars... My suggestion is to use something like Waves C4, or any frequency based compresser, and squash the range from about 125hz - 700hz. add a slight boost somewhere between 1.5k - 2.5k, and maybe a high shelf if you like the way that sounds.
Vocals - these just need to be more prominent in the mix. I mean yeah, its metal, but I still would like the CHANCE to try and understand the singer
All in all, not a bad job, just needs some tweaking to get there.