Well, one thing it needs is to be slightly more -responsive-.
By which I mean, things you do need to have noticable effects whether or not you do them as part of quests. For example - Recently, in my game, I killed Barzahl, and... Well, weird things happened. Not surprisingly, the Barzites started attacking me on sight - but surprisingly, so did the Awakened sympathizers and Awakened spy in North Rising Gates! Hostility needs to be painted less broadly than region by region - I don't know enough about programming to really know what I'm doing, but it seems to be like it should be possible to make more specific changes - attacked by the guards and not by the civilians, for example.
In fact, I KNOW you can do that because you did it in the Qurem-usss (or whatever the Taker stronghold is called) power supply - the Power Golems don't attack you even if they're right next to Guard Golems or Miner Golems who are attacking you, and they also don't attack the other golems or vice versa. If you applied that script to 'noncombatants' in towns, things would have more versimilitude.
Plus, more events should trigger those text boxes - When you kill a faction leader, you should be instantly aware of what a profound effect you have just had on the area. Maybe guards flee before your profound power. Hell, maybe you can even dominate the town and make them pay tribute.
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I want to second the earlier request to be able to speak to your creations. It would be a convenient method of setting their base A.I., and it could be very interesting when dealing with intelligent creations such as Drakons or Eyebeasts. If your creature begs for a second chance when you absorb it, it forces you to really confront the morality of what you're doing.
Pack animals! More specifically, Pack Serviles! I want to see outraged Awakened trying to talk your loyal shaped steward in to seeking freedom, and then outright rioting a week later when you casually menton you absorbed him to free up the essence.
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Creatures who join up with you, such as Xander or Herst Blade, should also be 'talkable'. Additionally, they should kick up a little text box when they die, and open up a quest to notify their next of kin.
In fact, they should be open for more quests in general. Imagine if you take Herst Blade in to the Taker town, and his old commander recognizes him! The town might riot to see you dominating him in town, especially when he defends you from them! Or if you take Xander, a free servile caster, to meet Zakary!
There's a lot of opportunity for inter-character interaction that is lost due to admittedly inescapable limitations on free time to program and cash. If possible, if you get enough cash out of Geneforge 2, I'd love to see more of those opportunities taken in Geneforge 3.