Some interesting thoughts here.

I have both solo and tandem and will add they are all rigged for flyfishing. My tandem is a beast. Approx. 16' long and 70 lbs. it actually has the third middle kid seat. It's a ocean kayak cabo sit on top (all mine are sit on tops). I use it in freshwater. Your paddles are not going to hit when using this thing. You could not flyfish two at once out of it. The bow person flyfish's the rear holds position or uses a spin rod. If your getting it for flyfishing you want some space between the two paddlers so don't get one of those solo length tandems.
My solos are always the first choice for fishing. The tandem is nice because you can cover ground fast and easy say.......on one of the Great Lakes for Smallies.
I have not found a canoe I feel comfortable in yet compared to a sit on top wide kayak.
I don't know what to tell you ? The tandem yak is not my favorite rig. It is very heavy compared to a canoe. A canoe really kills my knees with the seating as compared to a yak and like the yak it would be very hard to flyfish two out of it at the same time.
I think you need to try both. A 14' - 16' wide stable sit on top yak with seats and a wide stable 16' or larger canoe with seats & back rests. Again you will not be able to "flyfish" two out of either.