I've been playing around between these models recently. I've used a late (1980) Marshall JMP 2203 as a "do anything" stage and recording amp for about 30 years. I've had a couple of backups, a 2204, and a few other Marshall 50 watt heads too (all now sold aside from a JMP 50 watt 4-prong). I am so glad they are now modelled in the Axe FX III, as they have been an intrinsic part of any rock/alt rock/indie etc. that I have played over so many years. I got close with tweaks, but an "oven ready" 2203 is an absolute blessing!
Fractal model-wise, you'd think they are much more similar than they are in real life. In the modelling versions, 2203 has a bigger and tighter bottom end, but beyond that they are pretty similar sounding. In real life, both amps are insanely loud unless attenuated, but the 2203's bigger and tighter bottom end is supported by twice the power, and some really heavy duty power and output transformers when compared to the 2204. The 2203 with a 4x12 can be felt in the trouser legs much more than the 2204 at stage volume - it's a unique experience! Hearing the models side by side in the Axe FX doesn't really do justice to this (unless you are plugged into a mighty FRFR system, with the 2203 set for at least 3 dB more output level I guess).
I'm tending to use both models in a similar way to the real amps. For me that means gain around 4, and master volume around 3.5 for the 2203, and 4.5 for the 2204. As
@aens says, they can get really bright, but I tend to control that with treble, middle and bass controls, and try to keep the presence up as high as I reasonable can. If you turn the middle up very high it tends to disable the treble and bass controls' range a little, in common with a lot of Marshalls of the era. Going much higher than 4.5 on the master volume makes them sound "honky" in the lower mid range to me, and with a real 2203 that honkiness can also be pretty painful. Might be some of the reason I have tinnitus nowadays.
I don't particularly like the sound of these amps through the late 70's Marshall "1960" cabs that they came with (G12T-65W, or were they 75W?) A real shame as the only 4 x 12 I still own is a 1978ish Marshall 1960A.
My preference for IRs are G12H (30 watt) and G12M (25 watt) in 75Hz and 55Hz low resonance versions. There are some nice examples in the factory cabs from a few different sources. They have warmer mids, and less emphasis on bottom and top.
@aens, you might find trying these loses some of the "hi-fi" brightness, but I'm not all that familiar with late 80s Marshall cabs, so it also might not!
For me it's 2203 all the way between these 2, but it's my favourite "real" amp in a very long life of guitar playing, so that might just be blatant favouritism.
Liam