I know of some bike tourists who have remained in Baja a little longer just to do this loop. The big difference is that after Buena Vista they stick to the main road into San Jose del Cabo/Cabo San Lucas. In spite of its beauty, the off-road section right after Buena Vista (around Parque Nacional Cabo Pulmo) seems to me will be demanding due to the sandy terrain in long stretches and lack of services (water!). There are isolated homes and open campsites in that area but only reachable by 4X4 vehicles to carry supplies for days. Do research it further.

The option to fly into SD to do Tijuana bound south would be OK if you plan to ride and bus. Baja has some awesome stretches but there are some long ones that just suck (boring, desolate, etc.) It will get old really quick, especially if wifey likes touring a bit but would rather do/see other things.

Other routes you might want to consider for touring in Mexico (all serviced by Alaska Airlines):

1. Puerto Vallarta to Guadalajara: go inland to avoid horrible route 200.
2. Mazatlan to Guadalajara: Villa Union to Escuinapa (along coastal route)-Mexcalititan-Tepic-Tequila. You could also cut it short by going to P.V. after Tepic.
3. Guadalajara Airport - Lake Chapala area - Zamora - Patzcuaro Lake Area (including Lake Zirahuen) - Bus to beach resort of Ixtapa/Zihuatanejo to spend a few days before flight. I recently routed this one on MapMyRide.

Out of the three above, I would favor No. 3 hands down, then 2 and then 1.

In Mexico I would recommend >32mm tires due to conditions of some paved roads, cobblestone streets or even scenic dirt sections that might interest you.