Hi.
That's the same problem I'm facing at my house, multiple levels, also the radios don't have enough coverage to reach the far end of the same floor (PA's radios do, but I only use them on the GW and MQTT GWs, can't use them on battery powered sensors for obvious reasons), so the multiple gw distribution system should be an ideal solution for me and people living in "castles" or "Faraday cages" XD
Currently I have moved from a serial gw to Ethernet and MQTT gws (one Ethernet and one or two MQTTs), I find the Ethernet GW to be more stable than the MQTT ones (Client or Broker, same DIY PCB, I just pop out one nano and place the other) , your scenario 1, also some messages get mixed from time to time, even using different channels. Some times the GWs stop looping and I need to restart them, funny thing is that connecting to them in order to debug if they are running seem to jump-start the loop again.
So my vote goes for scenario 2 also, plus, it should be interesting for the Ethernet GWs to act also like MQTT Clients and/or Brokers, because the IOT community is clearly taking that approach in their effort to "standardize" all the chaos that exists today. I think we should keep things as simple as possible, I've read this post:
http://forum.mysensors.org/topic/887/future-network-topology-for-discussion
And I think it's a superb idea, clustering the whole network into more easy to manage subnetworks, each one with a different topology connecting to a Network (TCP) controller through their GWs, all the complicated stuff should be done by the "Controller" the subnetworks should be as dumb as possible, leaving the heavy duty processing to the controller.
I know this isn't much, I wish I knew more about all of this, but I hope my experience will be useful.
Regards.