So, in the interest of divorcing flavor or theme preferences for monoclan decks or not from the discussion, as there's no accounting for taste, I'm interested in hearing what the actual design advantages of monoclan (excluding out of clan cards) are. What does it achieve in a game design sense?
From where I sit:
1) It funnels decks down specific channels, within which a subset of options may be available. So you have factions A, B, C, D, E, F, G, H, etc. within which there might be two or three "themes" (as they were called by AEG), so decks effectively look like A1, A2, A3, B1, B2, B3, etc. This can be desirable for manageable testing, and/or simplifying meta and card pool analysis.
2) It allows a wide variety of cards within a faction to have abilities that would be potentially abusive when mixed liberally with another faction, as it can be made impractical or impossible to mix them. So, as a simplistic example, a faction might benefit when its own cards die as a reaction, while another faction makes its cards die as a cost for some ability. Combining them would result in double dipping off the death benefit. Obviously, many such synergies can be more complex and less obvious, but the point is that separating such synergies by faction provides a way to include abilities in a game that, if combined in play, would be detrimental to balance.
Now, my thinking is that in the case of point 1) A1, A2, A3, B1, B2, B3, etc. is a less interesting meta than Aa, Ac, Ad, Ba, Bb, Bc, etc. And that's not even considering you can still have sub-themes within clans, so it's A1a, A1b, A1c, A2a, A2b, A2c, B1a, B1b, etc. etc. Available decks are multiplied. Testing becomes a little bit more difficult, as there's a wider variety of options to take, but at least in FFG's case, there's plenty of established infrastructure that have tested games with similar approach. This, to me, produces a much more interesting and variable meta than a more restrictive "faction with subthemes" setup.
To point 2: This is easily solved by "Loyal" mechanics which exist in various FFG games, that prohibit specific cards from being played out of faction.
So...
What else?
Again, please leave preferences for monoclan or not out of this. Obviously, design is incentive, so it's a given if you want monoclan incentivized, privileging monoclan achieves that. Likewise the reverse.