So maybe they don't allocate funds to the development of an expansion as extravagantly as would for a base game that was still doing well. I don't know. I still think it's a possible explanation.
Again, let's not speculate too much over the financial and budgetary situation over at Firaxis, I doubt most of us are shareholders here.
What we
do know is that BE was highly anticipated for a number of reasons, not least of which having to do with the fact that it was Firaxis' first sci-fi/off-world themed 4x since SMAC. I don't think most of us were expecting SMAC 2, but we were anticipating a quality installment from the company that brought us SMAC.
Now we can debate why exactly the numbers started dropping off far more quickly than Civ 5 did prior to GoK, but I think it's a stretch to suggest that it led to the BE team having their budget/resources cut just short enough that they could put in as much as they did, but
couldn't manage adding a few more unit models.
As Galgus pointed out, it's seriously unlikely that would break the bank. And as GenEngineer pointed out, it's not so much that they were left out, but rather that no explanation was even attempted.
Seriously, watch the hybrid affinity units video. McDonough actually says, "I don't think we have hybrid upgrades for air units."
Not even sure what to make of that.
It's somewhat disconcerting when lead designers seem unsure about their own game.