I tend to play with 4-5 stock, low items/Smash Ball only, infinite time. I also play on any stage and not just Final Destination, and occasionally play with items on high. But that's just my silly way of playing. If you're doing a "just for funsies" tourney, I'd recommend these rules here, and maybe turn items on a little higher. But for a real tournament, I'd turn items off, include the traditional 8 minute time limit, and only play on stages without much of a random factor.
But in Smash 3DS's case, because blast zones seem to be wider and recovery seems lots easier, I'd lower the stock to 3-4, and any stage with a Final Destination variant are able to be picked.