Another thing that we're all missing out on is the ability to test the waters on these ideas. Dark Vengeance was a boxed set with Dark Angels and Chaos forces, right? They added two subsequent expansions for each side, right?

Imagine giving the next boxed set a limited run expansion that includes Adeptus Mechanicus forces with a rulebook for AM allied formations. How many want to bet you could sell that boxed set out in 5 minutes? Of course, you'd have to give something similar to the other side, too.

Just thinking off the wall here, imagine a Space Marines vs Tau boxed set. 5 Assault Marines, a chaplain with a jetpack, a tac marine squad with ML and flamer, and either a Dread or a Terminator squad with AC. For the Tau, a Crisis suit commander, 10-man Kroot squad, Fire Warrior squad, Stealth team, and a pirhana or something. So, take that as the basic boxed set, it's like 450 points for each side, and not a perfect HQ + 2 troops for the Marines, but whatever.
Then add an expansion. Limited release. Add your Kroot mercs to the Tau side as one limited run boxed set, and add Adeptus Mechanicus to the Space Marine side. Just maybe two units for each of these boxed sets - sell 'em at $90USD with 7-10 models (at least one of which is unique, or has unique options), and with special rules for the detachment, just like in the new SM vs Tyranid boxed set.

Or you could make it Imperial Gua... Astra Militarum vs Tau, and add Imperial Assassins as the boxed set for the Imperial side. Not like you need a whole rulebook for that, but you could sell 5 models and a rulebook for $90USD really easily if you were including all your assassin models and rules. EASILY. Especially if it has rules for a detachment that can be attached to any Imperial army? Who has an Imperial army that wouldn't jump all over that boxed set?

Best of all, you could do Sisters or Grey Knights vs. Chaos and add your highly sought after Chaos expansion with detachment rules, and add an Inquisition expansion. I always assume that GW wants to keep the number of models in the boxed set down in order to maximize the profit, so going with expensive (points-wise) armies like Grey Knights would make it feasible to sell a boxed set that included just 12 models per side for $125USD.

Anyway, that's just me sharing my early morning, post-breakfast thoughts.