Thanks quozl. Based on that, here are some of my thoughts on the nitty gritty.
I like the idea here of integrating the two games as a whole, rather than making either subservient to the other. My interpretation of how it's done:
A pure heroscape army plays exactly like it would in a game of Heroscape (no spell deck or summoning)
A pure MtG:AotP army plays exactly like it does in arena (essentially, every OM is on the planeswalker--I would probably rule that a planeswalker can lose an OM like anyone else, but others might differ)
A planeswalker is a figure, and has an army card, but is not a hero or squad figure, nor is it unique or common. A planeswalker is also inherently immune to permanent mind-control effects. When negated, a planeswalker can still cast spells and summon units.
All Heroscape figures are "creatures"
Heroscape figures cannot be unsummoned, (except perhaps the Rechets, since they have a mechanic for being reaummoned)
Magic:AotP figures do not belong to any general
Heroscape figures do not belong to any "color" in magic
In a mixed army, Heroscape figures start on the board alongside the planeswalker
A planeswalker of the appropriate color is required to summon AotP units
Etc. Basically the idea is to make as few modifications to the rules of either game as possible.