I think Neo's choice to save Trinity instead of humanity at least hints at the Architect using morality as another form of control. If the system is immoral, but has removed all moral forms of resistance, the only remaining forms of resistance are immoral. Thus saving Trinity is the only choice that rejects the Matrix.

It also demonstrates a flaw in the Architect's thinking. The One is the remainder of an unbalanced sum of human choices, a human embodiement of free will, in effect. The choice of save Trinity or save humanity is supposed to solve this problem by presenting a choice with only one possible conclusion, but by his own statement the Architect cannot account for human choice. In other words the One by his very nature won't always chose the "correct" option.

Personally I find this a lot more engaging than the usual "hero finds a third way" solution. In part because it's different, but also because it requires more thought to understand than just like, discovering yourself and punching extra hard.