I've always thought that plagues never happened often enough and they weren't very complex. Simply 'outbreak on planet x', send medical ship to planet 'plague cured', the end. Plagues go down for the count wwwaaayyy to easy.
Here's an idea: 2 different types of pathogens, say plagues and viruses, just to add some diversity. Next they all have different levels, so level 20 plague/virus is much deadlier than level 5 plague/virus. There'll be a 'death'(can't think of the right word at the moment) factor which indicate what number or what % of population dies. Also, an evolution factor, depending on the level, the plague/virus mutates at different rates. So at level 1, mutation factor could be every 5.0 years (very easy to kill), but if left untreated after 5 years, it would mutate into level 2 and its 'death' factor and mutation factor also change to make it slightly more deadly. Of course, the game wouldn't start off given you a level 20 plague with a 'death' factor of 0.15 and mutation factor of 0.5 years.
In turn, this means that medical technology would also have to change. Different types of facilities to find cures at different rates(this could be stackable to get bonus antibiotic/antiviral shots.) So there can be an element of urgency where you have to discover a cure for a certain level plague/virus before it mutates or the vaccine you discover is useless and you have to keep on studying to catch up. That's why it will be good to stack the abilities of the facilites.
You see, reading a Biology textbook has more uses than just for academic knowledge.
