How in depth are you looking? You can do some pretty crazy things with events if you're into that. But you need an idea first.

Got a Shadow Plague idea with some custom victory conditions, but I was thinking about adding more transmissions or symptoms possibly. I just want it to feel like I didn't tack on some custom win traits and nothing else.

Well, if all you do is tack on a few custom traits and add a few win conditions then that's exactly what it'll feel like. If you really want to make a good scenario, you should start from scratch.

The premise of a time travelling vampire has good potential, so the gameplay should be built around the concept.

Maybe instead of a traditional cure, there's a timer that ticks up each day from the very beginning (representing an event that will happen in the future) and by performing certain actions you can set back the clock.

Maybe you can "borrow" resources like DNA or disease stats from the future, increasing your stats for a certain time period but reverting them back a certain amount of time later. The Nano-Virus has two traits like this but you could make it your plague's main gimmick.

Maybe you can even incorporate saving and loading into the game itself by setting certain conditions that are randomly determined at the beginning of the game but are not revealed to you until the late game when it is too late, forcing the player to reload their saves and change the past!