As an orthodontist, I have had the same thing occur in various cases in the past. The important thing to consider here is that your doctor is willing to use whatever means necessary to complete your case...i.e. give you the best possible outcome. I encourage you to focus on the results and not the number of trays you will be wearing. Invisalign is a process where teeth are incrementally moved into there ideal location. This process can only be accomplished predictably by moving the teeth a maximum amount per aligner. This is probably why it ended up taking 12 aligners instead of 4. To attempt to speed up treatment could result in less ideal result. Hang in there
Typically, 2nd premolar spaces can be closed by protracting (shifting) the molar. This is usually successful but may require the use of advanced orthodontic techniques. My bigger concern is the treatment recommendation for the central incisor. Before any decision is made regarding your son's tooth, I would strongly advise a 3D image of the area in order to make the best decision for your son's treatment