So, now I use Micron's brush pens. I really like them - they're multidirectional and disposable, so they don't need to be used in a certain direction, nor do they need dipping or refilling. They're archival, don't bleed, and pretty easy to control. The only downside is the tip starts to wear down after 5-6 pages. There's still ink, so I begin to mark the older ones for use on thick, straighter lines, like walls and such. My scanner is bright, so occasionally I have to tweak the levels in photoshop to get the lines pure black again.
I've heard about the Tombo brush pens, and I might look into those when my current stock of Microns runs out...
I dearly love bristol 2-ply paper, but it's too expensive. I bought a ream of heavy cardstock (I forget what weight, 90 or 120, whatever the highest they had was) and found that it works just fine. Very little and easily controlled bleeding when I color (alcohol-based markers). I never found a considerable end-product quality difference between brison 2-ply and the cardstock.

