OK, I've been doing a bit of research on this topic myself. What I'd really like to see, obviously, is a thunderbolt hub or splitter, etc. There appears to be none, although I haven't seen anything saying that technically its not possible.
That said, I have 3 external monitors hooked up to my mac air (mid-2013) as follows:
My main monitor that I use all the time - Hooked up to the thunderbolt port.
My other two monitors - which are used more for reviewing documents, etc. - Are connected to a Diamond USB 3.0 Dual Head Display adaptor Model DV100 (it took me a little while to find drivers for this for the MAC, but they are out there). This is a USB -> 2 monitor solution (it has two ports - one DVI and the other HDMI).
The resolution I get is:
Main monitor - Asus VE278 - on Thunderbolt: 1080P
Second and third monitors - on Diamond device - Dell 2009W : 1680 x 1050
This is the resolution I was able to get on all three monitors when they were connected individually, so I believe I am not losing anything there.
1. Every time I reboot they default back to being mirrored. I have to hit Command F1 which puts them into extended display. Occasionally, I also have to go to display settings and rearrange them. An apple tech told me this is true of USB type devices, as Apple first loads the display settings, then the USB ones. So, when the USB settings are loaded, its too late to set the monitors the way they last were. This is annoying, but I'm getting used to it.
- As with any USB connector, the monitors refresh rate is a bit slow. With my particular setup, I don't notice this. Any videos I play are on my main monitor (on the thunderbolt cable), which works fine. If I were to try to play a movie on the other USB ones, it would be either very choppy, or would not play at all. that said, the other monitors are fine for reading email, typing documents, etc. For that purpose, they are fine.
As a side note, my monitors happen to have USB ports plugged into them. So, the cabling is actually pretty funny:
Computer USB port -> Monitor 1
Monitor 1 USB #1 -> Diamond device
Diamond device (HDMI) -> Monitor 1
Diamond device (DVI) -> Monitor 2
Monitor 1 USB #2 -> Monitor 2 USB input
This leaves 1 USB port free on my computer, which goes to a USB hub. It also leaves several USB ports available on my monitors, which I am using most of...
I know this isn't really the direction you were trying to go, but hope it helps.