I've been gigging with a large board (20+ pedals) for the past 4 years. I have to say i've never had any of these problems. I use blending and.... well, lot's of stuff to keep my low end, or boost it, or cut it when I like. Basically, it came from wanting a big live sound with only one guitarist, and I think it works really well. At first, I was ok with a couple of distortions and a blender, but then I started mixing our CDs and realise how much I really wanted to do with my bass sound. When i'm mixing, I like to boost the low end for choruses and heavy riffs etc, so I bought an EQ pedal to do this. That's just one example of a practical use for pedals that has nothing to do with novelty.
I guess if I was in a band with two guitarists then I could cut it down to a limiter, a blender, an overdrive, and two EQs, but that's the bare minimum. I suppose some people have these facilities built into their amps?
Oh, also, I am using a guitar amp for everything above about 800Hz. Maybe this helps?