Magic System
If we want a story about a necromancer, magic is implied. A couple of theme and setting questions first:
How prevalent is magic overall? Is it otherwise non-existent, are necromancers/cultists known of but not others, are there other kinds of wizards but they're relatively rare, or are we in a D&D-like setting where you can actually go to university to become a wizard with enough study (in which case the book provides evil shortcuts).
One of the first three I think. I'm leaning towards "necromancers/cultists are known but not others" personally. Gives a nice little tinge to the whole thing. There might be a secret corps of state/church sanctioned forbidden spellcasters even though the magic is otherwise publically condemned. Or something like that. Could get some interesting stuff that way.
Broadly speaking, how is magic done?
Detailed Spellcasting: You need to know exactly what you're doing, and there are steps you can cock up which cause the spell to have no effect (say the wrong words) or result in horrible side-effects or consequences (make the wrong offering). [I favour this one.]
Mana Limited: You spend a certain amount of undefined intangible 'essence' to cast a spell, which you regenerate with time or by sleeping.
Reagent Limited: Casting a spell expends tangible resources or has tangible requirements that limit it. You need sufficient vespene gas, or have the amulet on hand. [I favour this one.]
Could we have a combination of these three? Mana limited could be dropped though.
Combat
How prevalent should combat be? In a setting in which your primary focus isn't being a tomb-raiding mercenary, how often should combat occur? Should it be more or less non-existent so long as you don't throw yourself into combat situations?
How lethal should combat be? Should it be D&D level lethality (you lose 5 hp! you do 3 damage!) or closer to DF or RL lethality (you get stabbed - you are dead!)?
How involved should combat be? Should it be "You have 85 Swords. You have a 135% chance of hitting the mudcrab. You do 6 damage!" or more along the lines of "You are an Expert Swordsman. Right now you can a) slash at their torso, b) try to disarm them or c) wait for their attack and riposte."?
Somewhat uncommon. I was thinking more intrigue, building up our forces, playing the political game and the like, till we have a grand clash of armies in the open. Stuff like redirecting the inquisitors against our lifelong rival, the neigbouring duke, by planting evidence of cult activities in his basement, subverting Church Necromancers, bribing the pope to excommunicate the king, etc.
We might encounter the occasional tomb guardian while going ah... loaning the possessions of the honoured dead, or the inquisitors might come knocking down the door, something goes wrong with a summoning and we have to fight off a beastie from the great beyond, a assassin manages to sneak past our horde of the undead etc.
Combat should be somewhat lethal, provided we can do stuff like shuck off our mortal coil and possess the nearest schmuck, or something like that, at a great cost to ourselves of course.
I prefer the second, more narrative based style of combat. It should be simpler too than writing a actual combat system into the code, probably. Or keeping track of one if you don't literally write it into the program.
Also, it's ahead of time for it, but I was thinking about the main arc and thought about the idea that the book is all in unknown writing, but your [great-grandfather?] has pencilled in notes in the margins. A side element of the main arc could be questing to find his notebooks with translations and notes about his own work with the book before consigning it to the family tomb.
Rather than questing for our ancestor's notes (he couldn't have been that great in the end after all, considering he's dead
1 and all), which would remain a theoretical possibility
2, we instead try to decipher the language ourselves. Whether bargaining with summoned demons for linguistic lessons, spending some of our dwindling fortunes on rare books that'd help teach us the language (has the benefit of not needing to deal with those untrustworthy demons regarding these sorts of sensitive matters), or finding a scholar to translate it, perhaps by threatening to kill his entire family if he doesn't?
1: This suggests a interesting plot twist to me. Our ancestor isn't quite all the way dead yet, perhaps his spirit yet lurks at the edge of death, waiting for a foolish descendant to wander deep into the catacombs so he can use the blood-relation to usurp their body.
2: Perhaps related to footnote
1?