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You know what, great. I bend to the masses. You win. Thanks for the feedback. I'm done here.

Sorry OP, but you need to learn when to bow out and admit that people simply don't like your idea. It happens to me too, and you won't get anywhere by stubbornly telling everyone that your idea is good if clearly no one thinks so, and you have not defended the horrific logistics of its implementation.

Also, it's bad form to open an idea thread and request that no one tell you the idea is bad.

Furthermore, the direction you've taken both SoB and BT in this proposal would infuriate players on both sides. Why do you want to do that? Templars players love their fluffy 3000+ marines (which would have to be gone to allow them to work with the inquisition), not to mention the fact that Templars will not even work with a psyker Inquisitor. Witch Hunters players (imho) probably wouldn't be too happy becoming another MEQ army.

Then, there's the balance issue. Given the complex rules that exist in both armies right now, you'd either have to gut both codices and start with a completely new set of rules (at which point you might as well start a new faction, or invent some new soldiery for the Ordo Hereticus), or you'd have to implement a slew of restrictions to prevent people from building exploitative, overpowered lists.

Sorry sir, but I don't think your idea is workable.

So to answer your question: "Ways to make this work," I'd say: "Too much trouble to even try, and not worth infuriating fans to do, even if it were easy."