I usually sit in quarter lotus on a zafu which is on a zabuton with the calf of my left leg on top of the calf of my right leg. Usually I get out of this position because of pain in the medial part of my right knee or pain from the meat in the legs being squished for so long. It usually starts around the 45 minute mark.
When I switch the legs, ie with my right on top of my left, the bottom part of the leg below the knee falls asleep after about 20-30 minutes. It falls completely asleep so when I get up it feels like a dead weight and it has no sensation. The return of sensation brings with it quite a bit of pain.
I like to sit the first way because I can sit for longer and there isn't a lot of pain at the end. I would like to sit half-lotus but my ankles aren't flexible enough yet and they get really painful in this position. Not only do our hips needs to be more open, but the ankles need to be very flexible to sit in more advanced lotus positions.
Seiza feels more stable than a chair because there's more surface area of the body in contact with the ground and seat. Personally, I get pain in the right knee pretty quickly so I can sit longer in a chair. YMMV and I suggest trying one out.