I don't consider myself an expert in subwoofer. I have never compared the two either.
It depends what you are looking for.
1) If you want even in-room frequency response in different seating positions, then I would go with duals. Keep in mind that it takes a little work to set this up.
2) If you want sub-20Hz bass, two 350's will probably not hit as low as a single EP500, even if you colocated the subwoofers. Also, having two subs stacked or next to each other, does not look aesthetically pleasing compared to a single sub, IMHO.
3) If you get two 350's, you won't have the benefits of the DSP.
Personally speaking, I believe in the laws of parsimony. If #1 isn't an absolute priority for you, then I would go for the EP500.
I'm curious to hear what the experts would say.