I own both workstations, though I am not really sure how much relevant info I can provide. I use them mainly for sequencing with a computer, so only have limited knowledge of using them. I'll just say everything I know. Sorry for the extraordinarily long post! Here goes...
Keyboard Feel
Both keyboards have a very different key response. I know people who swear by the MoXF and think the FA feels like a toy. I am actually the opposite. I prefer the FA keys, especially for the kind of stuff I do like fast synth work or funky rhodes/clav stuff, which the FA is really good at. The MoXF feels stiff to me. I would be careful though, because the FA tends to have an issue where the pitch bend joystick will literally start to wear out internally, which will offset your pitch bends and make it impossible to use effectively. Some people have this issue after a while, others don't. My FA's pitch bend joystick is so bad now that if it gets bumped, the whole keyboard gets knocked out of tune. I've just been too lazy to get it fixed. The MoXF's pitch bend wheel doesn't seem to have these problems but it feels too stiff for my liking. As for weight, the FA is by far the lightest.
Synth Sounds
Since you seem to be after synth lead sounds, that's actually a grey area between the two for me. Roland advertises its supernatural synth technology meant for making great synth sounds. It's not much more than a glorified version of their PCM sample engine, but any Roland product that has the supernatural synth engine (and the FA is one of them), is going to give you a huge selection of synth sounds, both onboard and external expansions which you can put on the unit. I'd recommend checking it out. I don't think the supernatural synth is quite as good as advertised, but it's not bad or anything. The MoXF has its fair share of synth sounds too, which have a flavor I like more. The problem though is that its engine doesn't seem very lead-friendly. Samples retrigger too often, producing a sort of jumpy sound, and as much as I like Yamaha sounds, their synth leads seem to be sort of lackluster in terms of playability. They sound okay in music but if isolated, you can hear more deficiencies.
Organs
I think you also mentioned organs. While the FA has a supernatural organ module, I don't like it as much as I wish I did. While I think it sounds good in a mix, something always sounded wrong about it in certain areas. Different timbres can be found in other sections of the FA's instruments which I like more. The MoXF has some decent organs too.
Other Sounds
In general, I prefer the MoXF, but there are exceptions. Both have their own variant of piano, strings, synth, bass, clav, electric piano, etc. and I tend to lean toward the FA's take on those, though the Mo can do them pretty well too. I think the Mo excels at guitars, especially acoustic and clean electrics. The FA's distorted guitars are better to my ears when it comes to playability, but the Mo's are more aggressive and intense, and sometimes go way overboard. Also, while drums on the FA and MoXF have their own distinctive flavors, and while I again tend to gravitate toward the MoXF, the MoXF does air too much on a heavy, overproduced sound for my taste. The drum sounds on both units are so radically different that it gives me this strange sense of contrast. I find the Mo is better for orchestral and cinematic work too. The FA, while it gets by and has some good sounds in those categories too, just sounds too sterile in that department for me, and is one case where the sounds aren't heavy enough, or just don't fit the atmosphere I'm going for. Keep in mind, however, that our preferences may differ. And, just because I say one of the keyboards has inferior sounds in a category doesn't mean that I think all of those sounds are bad. I am just outlining my overall opinions, nothing too specific, so don't blindly take my word or jump to black/white assessments too quickly.
Creating Sounds
Both keyboards allow you to create user patches, though the FA gives you more slots. Both keyboards allow you to adjust a host of parameters, and customize elements on the MoXF, or partials on the FA (they mean the same thing) to create your own sounds. And yes, both have quite a blind man's learning curve just to get around the menus as well. I remember the FA particularly being annoying because it always remembers your last place in a menu tree, so if you get lost, the only way to really start over or get your place is to turn the keyboard off and on again. I can't say whether the same is true with the MoXF because I haven't tested it enough. Both keyboards also have good manuals, which tell you about a host of shortcut commands to access certain items to perform different procedures. Do not dismiss these; they are extremely useful!
If you want more accessibility with the MoXF, you can try John Mela's Motif editors. They are PC applications which allow you to edit almost anything on the MoXF with the computer. I suspect the tool you would be most interested in is the MoXF voice librarian, though you can buy tools individually or in various bundle packages. All of the tools are screen reader accessible to a point. Though I've only briefly tested them and they do still have a learning curve, I think they are accessible enough to have some real productive value, and you'll certainly get a lot more information from the applications than from the keyboard. John is a really nice guy too, so if you have a question, don't be afraid to e-mail him and ask. Or me as well, since I'm going to purchase the complete MoXF suite of tools soon. The FA does not have such extensive third-party tools. I recall there being some sort of librarian for it, but I never tried it and don't know what it does.
Adding new samples
The MoXF allows insertion of a flash memory module (either the fl512M or fl1024M, which add the respective amount of memory to the synth for you to load new content like samples or waveforms for patch creation). I don't have a flash board yet but I will soon get one. The FA does not offer such expansion capability. You can, however, download free expansions for it on Roland's axial site, though it's not possible to add your own waveforms. Roland gives you more waveforms than the Motif but you're stuck with what you get.
Acting as Sound Cards
Both keyboards can act as an Asio-capable sound device which you can use to, say, play vst synths with zero-latency. I've tested both and apart from a few qwerks, they both are easy to set up as such, and the performance with both is good. I haven't done any huge tests to figure out if one is better than the other. But if you're after simple Asio support, neither would be a bad choice.
Other Options
There are other options which you may find useful.
While more restrictive in terms of editing sounds, the PSR-S keyboards have gotten really good, particularly the PSR-S970 which I own, and its little brothers, the PSR-S770 and PSR-S670. Then there are the Tyros keyboards which as you might know give you far more but are more expensive. What I use the PSR most for is its accompaniment sstyles, and its GM/GS/XG compatibility. I also like the PSR keyboard feel (it's somewhat similar to the FA), and I like the pitch bend wheel better as well. I've always liked the PSR and Tyros sound pallet better than the Mo. My favorite parts of my PSR's sounds are mostly acoustic stuff, particularly for soft rock, funk, jazz, country, orchestral, etc. I think a lot of their organ sounds are really nice because they have a lot of character. The synths are okay too, though I tend to like other things for synth sounds. Just keep in mind that these keyboards are not the same kind of workstation as something like the FA or Mo. They have a different feature set. ?For a start, I don't think they would let you create sounds like the FA or Mo would.
Because I do a lot of music stuff on the computer, I've been experimenting with other options that integrate more with a DAW. Depending on how you go about it, having such a setup might be cheaper than getting a workstation, though it will be harder to assemble everything since you'll have to do a lot more work to set things up. Nevertheless, I know people who do just this, both for music production and performance needs. If you are interested in info on that, let me know.
Conclusion
Personally if I was trying to decide between the two, I'd get the MoXF because of my favoritism for Yamaha sounds. But then again, your preferences may vary, and for synth sounds, I do think the FA might have an edge. My advice is to keep doing research. If you want to discuss it further, we can do that also. I have a fair amount of resources for both keyboards, so if you get one, I can hook you up with manuals and guides from an accessibility perspective.
I hope this helps!
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