When running a most improvised scenario (either something as ambitious as the Dracula Dossier or just riffing off a paragraph or two of notes), One Useful Trick is to have a copy of the investigative ability list for your game to hand, and check off abilities as you call for them or the players use them. That lets you see at a glance which abilities you haven’t yet used in play.
Then, look for opportunities to bring in other abilities. Treat it as a prompt, a challenge – “what’s the easiest narrative route in the game from this moment to the action hinging on Art History or Pharmacy or Flirting?”
Often, in improv play, you fall back on the sort of scenes that you’re most comfortable with; I can riff mysterious murders, spooky locations and sieges off the top of my head, but need to remind myself to do interpersonal scenes, crowds, or car chases.
Prompting yourself to bring in abilities you don’t instinctively default to is a great way to vary the scenes in your game. The players in my current Night’s Black Agents game, for example, are much more comfortable hanging back and observing, either by blending into the crowd, perching on rooftops, or getting full value out of all those points invested in Data Retrieval, Electronic Surveillance and Digital Intrusion. Tracking the abilities used reminds me in the heat of play to put in more interpersonal scenes, forcing them to use messy touch-feely abilities like Reassurance or Intimidation.
A neglected ability doesn’t have to be central to the game, of course. If you’re trying to bring in, say, Astronomy, you could just mention that the characters knows offhand that tonight will be a moonless and especially dark night; often, reminding players that they have a particular ability will start them thinking about ways to use those assets.
Don’t neglect General Abilities, either. If no-one’s used Cover or Disguise in a while, try to drop in some obstacles that require those abilities.