To clarify, "honeycomb" mission design is something one of our System Designers, Matt MacLean, suggested for Alpha Protocol. If it had been early enough in pre-production, we would have used it (and hopefully still can). It applies to a mission design where the player is giving an overarching objective (say, "force the Montaine troops to evacuate the border garrison") and then give the player about 5-6 "satellite quests" orbiting the main quest, all of which can affect the set-up or success of the central mission. The player can choose which of those 5-6 missions he wants to undertake, and they all react to each other and cause a reaction in the central objective as well.
We did this to an extent in AP (optional missions, missions affecting other missions for each hub), but there was much more we could have done with this system, and all other things being equal, it's my goal that it be a focus for at least one of our titles in the future, as it's a really interesting idea.
The disadvantage is it can get extremely complex if done improperly (special casing events), the advantage is that it's a better means of giving the player reactivity without a linear quest progression... and more importantly, it gives the player choices in how they want to complete the objective. They wouldn't need to do all 5-6 missions at all, and they could accomplish these satellite missions in any order they wanted. A speech character may simply target 3 missions that cater to diplomacy (say, sowing gossip or convincing soldiers or officers that the main capital is going to be attacked), and suddenly the garrison gets a high-level order to move its troops to the capital to defend the monarch.
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