I've done something like this before (and it went well), but I realized I over complicated it.
The Premise is we will be doing two simultaneous Franken Drafts in different channels. At the end, you will build a "powered" faction (4 abilities, 3 faction techs, one of everything else) from among the components you drafted across both games. This may (and probably will) lead to duplicate abilities at the table, which can spice things up in a surprising way.
A few clarifications:
-Slices will be pre-generated, drafted tiles won't do anything
-The speaker order in the "primary" game (the one where the game will happen after the draft finishes) will determine your position at the table. The speaker order drafted in the "secondary" game will be the order you pick your slice from the pre-generated ones
-If you draft the same faction ability in both drafts you can use both for double the effect, as long as it makes sense to do so (should be fairly obvious if it can or can't work)