I may be talking out of school on dacron because I've never used it, but one of the other advantages is its mildew resistance. The draw back to dacron that I see is that it accentuates all of the tack heads, hammer blossoms, and plank seams. The thicker canvas "softens" the effect of those anomlies making them less noticable and more aesthetically pleasing to my eye. That is important to me. However, on a new, tight, fair hull, dacron may be the best choice.
Use of the ekofill on canvas leaves the mildew question, unless you are using Rollin's treated canvas or find some way to treat the canvas prior to filling. (anybody know of a treatment?)

Although I believe ekofill has biocide in it, I always add some. I also add it to the primer mix. One other tip I can give on Ekofil is to use it very liberally on the first coat, so as to soak it as deep as possible into the canvas. Don't try to stretch it. It dries quickly, so you need to be fast and heavy with the first coat.
I haven't tried it, but have considered thinning it with distilled water to make it soak in better and possibly slowing the dry time on the first coat. Subsequent coats will not "soak in", as the first coat becomes a barrier.
Like Dan M. and Cavy, I have not had any issues with my own ekofill canoes or with customer canoes...(Knocking on wood!)