Magnaguard is built to help Sep Droids be consistent against JKR, so definitely use him when facing JKR. I typically use zNute over Droideka in arena because it helps boost B2's AoE damage and Droideka's single target damage doesn't seem necessary with G13 GG. Droideka isn't useless though. He doesn't have a taunt, but he should quickly become your healthiest Droid and one of the first to get mark from GG when GG goes under 100% HP.
Droideka shines in Geo TB too. I've had mine Basically solo a wave since clones don't have any dispels. They're also pretty fast so Droideka gets a lot of bonus damage on his special.