Well, I'm familiar with you guys, and compared to you I'm a wannabe, so I'm a little gun-shy about responding... but I have a similar struggle sometimes in our little amateur jamband, and appreciate the chance to hear what others think about the unique role of the bass in this genre of music.
Sometimes, I think I feel sucked into the same 'ol minor pentatonic (because we're all deeply programmed to follow it, and) because of where my guitarist (often unknowingly) places his emphasis. Even though he is consciously playing past or beyond the blues scale, throwing in lots of other notes that "don't belong"... the reality is that he is phrasing it such that the most 'important' notes often land right smack dab in that scale. Or at least that's my perception. So, I feel like if I stray too far, or resist too hard, I run the risk of not being there for him when he needs me, to keep it all a little linear and melodic.
One strategy I use is to carefully build a little tension by using some of his passing tones to paint a little weirdness underneath. Tim's are often 1/2 step up or down from the notes that are in the scale. I'll take little non-conforming phrases I hear, and repeat them, try, to turn them inside out, etc, sandwich them between more conventional stuff, and then ease back into the more predictable stuff through a back door before I've stretched it too far. Its risky because it can just plain sound wrong. But when it works, it sounds intentional and kind of esoteric, especially when the ouch is healed with a smooth resolve to the root.
But we're just a 3-piece... I would imagine this would be much harder to pull off with other guitars, because the tension can't really 'breathe' and hang there the same way.