One door would lead to the Source and allow Neo to smash the matrix, and save Zion (although Trinity would die). The other door would allow Neo to get back into the Matrix, and (perhaps) save Trinity. But if he chose that door, Zion would be destroyed and Humanity would become extinct.
If the architect was telling the truth, Neo had to choose between love of a woman and love of humanity. Two different types of love. Did Neo make the right choice? Was the architect steering Neo in a particular direction? Was it a good direction, or bad? Did Neo behave in the way the architect wanted?
Noen of this is clear until the third movie. Which I hope is better than the second.
The first door let him select 6 men and 7 women to make a NEW version of Zion and start all over again.
The door that led back to the matix (lower) would compound the errors in the Matrix that would result/risk the destruction of the entire human race.
Neo 6.0 took that door in order to save Trinity's life ... no other neo version ever took that route.