I am the OP of the thread and have had my SGSII for 1 week. Here are some initial thoughts and impressions of how the Atrix and SGSII...
I got the Atrix after the gingerbread update to replace a captivate. I bought it outright and it came loaded with 2.3.4. I still had my upgrade so I picked up the SGSII on launch day. I will go a few more weeks before deciding on whether the SGSII is "upgrade worthy". I am keeping my Atrix regardless. (I do not really know why I like it so much) I have not rooted since my captivate so the custom ROM's etc do not affect my usage. Would probably not use the HMDI etc since I have enough devices to play on my TV without using my phone.
Some quick impressions on advantages over the other:
Atrix-
GPS is faster and dead on accurate
Screen resolution, took a while to get used to it, but I like it
Battery life! 30+% longer for my usage than SGSII. I carry both phones in case I cannot recharge my SGSII.
Better Bluetooth with My Audi Q5 than SGSII. Not sure why, but I have dropped several more calls with the SGSII than my Atrix.
Build quality, just feel more solid
Updates. I understand the Atrix has been updated 4 time since launch
SGSII-
Touchwiz is tons better than motoblur in terms of integration and widgets. I use launcher pro but have been able to go a day on touch wiz which I have not done on blur. I hate that you have to have a blur account and sign back into it every time I switch my SIM from one to the other or when you just use on wifi without SIM card.
Camera. For all the reason shown in this thread. Pictures and Video.
Samsung stock extras- Such as settings on notification toolbar.
I get a 2500+ on quadrant for the Atrix and 3500+ on the SGSII but I have yet to see any practical differences when using the phones.
If I had to pick right now I would take the SGSII back and wait to see what is coming after the new year. I will try another two weeks before making up my mind.