Did you know that there are 3 326 400 possible quad-color decks combination?!
No, I didn't know that, and I'm not sure I believe you. I'm not sure what you mean either though.
There's 495 different 4-of-12-colour combinations. The number of different 4-colour decks you could build with singleton rules (allowing multiple pillars) is in the order of 10
12 (assuming about 15 non-pillars).
Sorry, shouldn't derail yet another thread with maths... back on topic.
If you want more few-colour decks, how about allowing multiples of the twelve 'basic' pillars, but still restricting QPs?
On the issue of upgrades, sticking to non-upgraded cards will give those who haven't framed for 1+ of every card equal opportunity.