If you wish to keep Gengar I'd remove Focus Blast due to its unreliability, and use Destiny Bond instead to KO something that is giving you a hard time. Timid nature would be nice as you can speed tie Latios at worst and Ghost Gem Shadow Ball can still OHKO it I believe. Maybe Substitute over Protect as it can allow you to dodge Thunder Waves/Spores. If you don't plan on leading with it much I'd stick with Protect.
I'd also think back to your matches. Have you used or did you find yourself needing an electric move quite often? Keep in mind STAB Shadow Ball and Thunder have the same BP on Gengar. I might be biased but I haven't really found myself in that scenario much, as such I'd probably go with something else, like Energy Ball/Giga Drain or even Confuse Ray.
For the last slot I suggest a Water type that maybe has Blizzard to abuse hail? There's a lot of good ones so I can't really make a definite suggestion.