I think it boils down to "trying" to be "uncommon" vs creativity. I faced similar problems with a few bands i've played with coz i play the bass quite unconventionally... but i do what makes sense. When i write my bass line, i think of myself as a GLUE as neversconcious mentioned.
I start off by just doing the roots, from there i'll start creating a motif from the vocals or guitars or a mixture of both and yet rocking hard and grooving with the drums, or simply just filling out the empty parts of the song with a motif when no one's looking =P whatever makes sense to me during the process, my purpose for doing this is to create a link between all instruments and to give the song an identity by bringing out what i feel is the most catchy part of the song.
I always prefer my bass lines to interact with the whole band. Of coz all these are subjected to changes according to the preferrences of my band, i will fight for my cause when i feel strongly for it but i will never let my style or my "uniqueness" get in the way of creativity and the music direction of the band.
For effects wise, i must say, if its creating emptyness like lack of the bottom end which i hear from many bassists using various very interesting effects and the sounds are clashing, then the band should sit down and figure it out and do "what makes sense".
Some muse songs i hear uses the keys and strings to fill out the songs and when u do the the bass effects without keys or strings, its usually the "quieter" part of the song where the bass rock out with the drummer but of coz there are exceptions like hysteria etc etc, but they managed to find a balance so that all instruments could be heard.
Clarity is a MUST if your using effects for bass and the sounds of various instruments in a band shouldn't be clashing. what's the point of adding effects that only sound nice when u play the song alone? =)
Ah... you talk of balance... with the nod to creativity.
And I think what's more important is how you mentioned - the band communicates. Talk... finding solutions, compromise and so on.