I find the F1s to be more comfortable as well (they would get my vote for most comfortable cans ever). The pads and headband material feel softer than what is on the MA900s. The MA900s headband touches only on one small area whereas the F1s seem to more evenly distribute the pressure. The MA900s seem to slightly clamp a bit more. My ears have a little more clearance with the F1s also. They both are exceptionally light. The MA900s build quality seems a lot closer to something in the $50 range. They just seem flimsy and I really am not that impressed with the feel of the material for the padding. The F1s feel and look a lot nicer. I love the metal microphone driver coverings. The MA900s are a bit sleeker and perhaps offer less of a geek factor and probably function better for listening while lying down.
I think the F1s are a supremely cool pair of headphones and are under appreciated around these parts. I would much rather listen to them day in and day out than a lot of other higher/high end headphones that I have owned and tried for use in my office (HD800s, LCD2s, AD2000s, HE-500LEs, RS1s, PS1000s, GS1000s, HD650s, and quite a few others). All of those phones has aspects of their sound signatures that ultimately I found disagreeable or too distracting. While I absolutely love the soundstaging and comfort of the F1s, the MA900s are just a touch behind there and seem a bit more than that ahead in terms of sound quality. They are not the last word in refinement or detail but nothing bothers me about them and there is plenty I like.
Both the F1s and MA900s are sitting side by side and I have completely gravitated towards Sony's newer offering. The other open pair of headphones I use at home are the Stax 009s, and there is no comparison there. However, the MA900s deliver enough of that high end feel to my ears that if I ever step back and truly realize what a ridiculous sum I have spent on hi fi headphones and components, I could scale back to the MA900s and an iPod and live a very content audio life.
I really like the Z1000s too and hope that an MA1000 is in the works.
As usual, that is just me though, and no one should ever buy a pair of headphones based on what I think.