Is it normal to treat my top and bottom teeth separately, waiting 3 years to continue, or is it best to treat them all at once?

With Invisalign, at times the teeth in one arch begin moving first, to prevent bite interference issues during the treatment. Nonetheless, 41 months of delay sounds excessive. I suspect that the upper teeth start moving at the 41st aligner, which is still a good 20 months into it, but not 3 years. Double check with your doctor on the timing of upper treatment start.Also keep in mind that Invisalign is an orthodontic lab, that provides treatment proposals and aligners based on the treating doctor's prescription, review and approval. As such, your doctor is the one who decides whether extractions are needed, and not the technicians or the doctors at the clinical support phone lines at Invisalign.In a long treatment time Invisalign case like yours there can be a benefit to using a limited fixed appliance at the same time as the Invisalign trays. For example, if it takes 20 aligers to fully rotate at tooth, adding a short section of braces for 4-6 months may shorten that part of the treatment, and cut down the overall treatment time. Good luck!

The folks at Align have a lot of experience, so their advice is likely accurate. You may submit an alternative to see if they think it would work. I would consider regular braces instead. Much more predictable and faster.