So, anyone here thought about options for object-altering magic that isn't Transmutation effects? Now, when I say "object altering", I just refer to altering the effectiveness of the mechanical article that the object is. For example, an Abjuration effect that makes an object have increased effectiveness against creatures of a particular kind or alignment, basically Magic Weapon, but applying Bane or (Un)Holy instead of a vanilla +1 bonus(to use not-necessarily involved 3.x-isms).
On the end of Conjuration, my thoughts are stuff like making a linked Ethereal duplicate of a weapon to make it have increased effectiveness against Ethereal targets and make it harder to break for all purposes, alongside layering a Shadow Illusion of an object over that object to make it better overall by re-defining the edge. Note that object is not solely about items, creatures(and spells) can also have it apply. Shadow Conjuration increasing Strength and Constitution, as well as granting temporary HP, in addition to Shadow Evocation being able to make Evocation-based effects more powerful.
In Necromancy, partially detaching the soul from the body could make one literally partially a ghost, gaining many of the resultant abilities of being a ghost(at higher levels(CL or higher-level equivalents for 3.PF, upcasting for 5e), it might give Wraith abilities), but the actual cause would result in a serious hit to Con(your soul is not properly attached to your body) and Dex(your mind doesn't get the feedback it should, nor do signals get through properly) The Cha boost, naturally, would draw plenty of use for the caster.
In pure Illusion(Shadow Illusion should really be Evocation/Illusion mixed-school affair), Glamers(to use a 3.5-ism again) can make an object have apparent properties that make it more effective, like being far hotter or colder and causing non-lethal Fire or Cold damage(Unarmed Strikes for creatures), or make it significantly harder to perceive and thus harder to avoid if the target fails the save against the Illusion.(and yes, I do think there should be Illusions that deal non-lethal energy damage)
I... Can't think of any Divination effects for just flat out items, because I can't think of a way to have a Divination effect only on the item, with no application to the holder, provide useful combat effects(LotR Sting ripoff, to identify things before hitting, maybe?), but the benefits for creatures are largely about combat-viable precognition and telepathy, knowing where an attack will land before it does. In 5e, this'd be a great place to put a "Use your Reaction to move 5 ft. instead of getting hit" effect.
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As for megadungeons being out-leveled? Find higher-CR equivalents of the creatures used, then rip off Bethesda and have enemies replaced by higher-level near-equivalents. Ghosts become wraiths, Shadows become Devourers, Skeletons become Death Knights, Necromancers become Liches, Ghouls become Ghasts then Wights and so on. If no such thing exists, make one. You should have seven level brackets of this, so that there's a range of three levels between bracket changes, enough to have there be easy fights before a bracket change, but not enough to result in stretches of really bad layouts. Maybe have the second bracket only be level 4, or the first and second be two levels long, and have the third run 5-7, if you're doing 5e, because of how big a shift Extra Attack and 3rd level spells can be.
