In my opinion there are no aural pros and cons. It's just a matter of what best enables you to position your drums and cymbals as you like combined with aesthetic issues.
Personally, I do not like drums mounted off of cymbal stands. I typically do not even like additional cymbals mounted off of cymbal stands. I own a couple of those clamp with boom arm deals and almost never use them--it seems like I can never get things positioned just the way I like them when I use those. The other cymbals get in the way, I can't get them angled right for me, the right height for me, etc. I prefer a combination of simple straight cymbal stands and simple boom stands--"simple" meaning "without giant, pyramid-shaped tripod bases, tubes like baseball bats, etc."--just something with a relatively flat base and relatively thin construction. To me, having those monster legs on every stand just makes it harder to position everything.
For my toms, I like Tama-style tom mounts on either a separate stand or a bass drum mount. I don't care about virgin bass drums--I always buy them with, or so they can accept, tom mounts (and I also buy them with cymbal mounts if I can find that, too). Sometimes I use the bass drum tom mount, sometimes I use a dedicated tom stand (same thing with ride cymbals on bass drum mounts versus separate stands). It depends on exactly what I'm setting up. I like having maximum options, and I don't like setting up the same all the time.