Occasional use of the flute could be cool, as well as just about every other available instrument. Taking Nightwish's 'Ghost Love Score' as an example, I would love to see Opeth utilize symphony for a piece or two. It would also be neat to see Opeth experimenting with their guitars more, such as using a e-bow, or even a slide sometimes. It would be cool on one track to have one guitar with a slide and the other one doing the sliding octave and full barre thing.
However, my biggest problem with adding flute is that they would probably get a flutist, and then employ him full time. I like Per and his keys, although there are a few select times on GR when it is like, "Ok, well Per is playing so he has something to do here". The only thing I don't like about Per's addition is there are parts that you can hear if they were used in the BWP and Still-Life days there would layers of lead guitars playing those sounds, and you miss that wall of sound effect. If there was flute player full-time I cannot help but think he would be intrusive.