Ive spent several years switching back and forward between different setups and systems trying to find the best high speed 68k/os3.x amiga setup, so this is a subject Im pretty well versed in.
To be completely honest though for every pro about one options there's usually a con or 2 as well, but for me amithlon has been what I end up going back to.
It depends on what youre wanting to do though. Do you favor apps and/or newer games, plus like to play some older games, or do you favor older games and use a few apps and/or newer games?
General rule of thumb is, do you want a retro "amiga" that can do newer things ok, or do you want a more modern amiga that can do the retro side ok? Amithlon +UAE will never be as fast and/or accurate as something like WInuae for custom chipset software, but give it enough grunt and its enough for all but the heaviest aga demos (ocs/ecs emulation is considerably quicker). UAE itself plays a bit of a part in this, and that's being updated (with cosnsiderable speed ups) for amithlon natve as we speak.
As suggested something like MicroXP can be a decent host for a dedicated emulated 68k box and does increase the supported hardware base over amithlon somewhat, but amithlons supported hardware isnt nearly as limited as its reputation. Ive tried on many, many computers over the years, and have never once found a system I couldnt get it working on. Things like sound, network, and gfx need to be given some thought thought, but that's pretty normal for alternative type systems, and is true for aros/mos/os4 as well.
As for ease of use, I guess Winuae has some advantages here. With amithlon youre completely at the mercy of AmigaOS and functionality needs to be found there. WinUAE will suppliment some of this through the host (usb, tcp/ip,p96,ahi,etc,etc.). Whether or not this is a good thing or not is down to the user, but personally I prefer it through the amiga os side as I both like to know my system inside out, and I prefer the extra flexibility it provides (try creating a 256x192 p96 screenmode (or any custom screenmode) in Winuae for example (you cant)).
AROS thus far is probably not the best option is 68k is a priority, which is a shame as it has great potential, its just not quite there yet unfortunately. Perfromance is a mixed bag,.... raw uae cpu performance is second to none for an amiga derived system (both because the hardware its runnig on, and as it has jit cpu emulation), but in practice it can be inconsistant. As often as not onscreen performance is inferior to amithlon on the same machine (and amithlon is emulating a 68k cpu and then emulating an amiga (including cpu again)). Given some time I suspect it will mature firther, but for a person who favors 68k Id wait before using AROS as a host (which is a shame really).
As for joystick support for amithlon support, this can be done a few ways. Poseidon, catweasel mk3, gameport (for supported sound cards) or if youre lucky you might find a ps2 or at joypad (as in a joypad that works of those connections, no playstation2). Theyre not common, but do exist (I use one). Typically a person plugs this straight into the mobo, and then plugs the keyboard into that (thats how mine works at least).
Id be lying if I said the game port option wasnt a pain to set up, but it can work. Poseidon Id expect would require a supported external pci card.
In short, Id suggest amithlon, but expect to alternate between loving it and hating it for a while until you get things working nicely
Im going to make a video of my amithlon box running all sorts of bits and pieces soon as I dont think there's a single video out there showing just how capable it is.
This isnt just a testament to amithlon's longevity, but to OS3.x itself. Given the grunt and some optimising/customising, and it stands up to the newer, younger systems nicely, only with 1000's of times as much software
