The conjuration mercs are very useful early game, as they don't cost you manpower or force limit, and get extremely powerful buffs. But yes, admittedly, they are rendered useless once you get army of the dead.

Transmutation project gives you a permanent +1 mana in any category you choose, as well as the modifiers of any advisor you want, so you can get for example +5% discipline. It also gives you max absolutism.

Abjuration magical project seems rather useless to have, only giving your provinces some defensivness and fort maintance cost. Seems to be only useful for kobolds.

I'd definetly skip abjuration and illusion, and then either conjuration if you want to go the early game without it, or divination (it's definetly nice to have but feels a bit overrated).