Why does no one use Droideka for any Separatist team?

It's more that if you have a better option like Nute or BB-8, someone has to go, and droideka is the least necessary of all the options. If you absolutely need to use Nute, BB-8, Wat, or any other option elsewhere, of course droideka is fine.

Droideka is fine and gets some use, but not where you expect him. In a Grievous Sep Droid team he is ok, sort of the standard lineup of GG, B1, B2, Magnaguard, and DDK. Eventually, however, that lineup isn't good enough on defense or offence so it needs to replace one, and DDK is the least essential of them all. So DDK gets replaced with Nute or BB8 or even IG88 sometimes to try to stop NS counter or work on offense.

Droideka does get used with Geos sometimes for offensive GL cleanups (Geos minus poggle plus DDK for example cleans up solo slkr). His main use, lately, in Kyber has been with Maul actually. With his 50% speed bonus a 250 speed DDK is 375 speed and goes first to trigger Maul's turn.

Droideka is pretty good in DS TB also.

If only our player-controlled version was anywhere near as terrifying as the NPC one.

We don't use him?
News to me; I use him all the time! I have a GG Sep Droid Squad and there's only 4 other applicable candidates. Makes light work of lots of common defences in TW, for one thing.