Problem 1: How do duos, trios, and quartets work?
I suppose you could calculate the QI of each individual element, but Pendulums give elements every other turn, throwing calculations off.
The simplest and usually good enough solution is to calculate each element individually and consider pendulums to be half of a pillar.
There's also the important decision which mark to take, and from which element take the pendulums. Usually the mark should be of the element that you need early, but with pendulums you get the pendulum's base element one turn earlier than the other one, so eg. fractal devourer with darkness mark and aether pendulums will have a bit more darkness, but even upped won't be able to field devourers earlier than turn 3. On the other hand, aether mark with darkness pendulums might allow a turn 2 devourer (turn 1 upped), but would produce more aether overall... if not for the devourers, that is. Of course playing upped alters these calculations a bit.
Problem 2: We need to take into account how long the game is expected to go.
If the expected TTW is ~7-10, then QI works perfectly. But if you run a stall, for example FFQ decks, then you'll have not enough quanta in the beginning, and too much in the end
Here the simplest solution, and the one most people are using I guess, is to find the best QI for a given type of deck. Generally rush decks work best with QI between 4 and 5, while control decks, denial, stall etc. work better with QI between 5 and 7. For rush deck, it is usually best if your hand is empty roughly the turn you win (eg. no excess quanta, no excess cards), so you can adjust QI trying to achieve this.
On the other hand, most slower decks shouldn't follow this path, since they need a lot of quanta in the beginning to take control of the field, and less quanta later, to keep the control. Thus naturally they have excess quanta in late game. One exception might be the decks using hourglasses to draw additional cards, so they might be able to use the excess quanta.