I own the Matrix GT800FX. Today I also received the Atomic Reactor 50/50 for a trial period.
I connected one channel of both amps, set the output to Copy L>R, and played for about a hour. I'm using an Axe-Fx II, and two 1x12 cabs with an EVM 12L in each. Here are my early conclusions.
SIZE and WEIGHT
The Atomic is larger (2U vs. 1U) and much heavier. I have no problems with it (combined with the Axe-Fx II in a 4U case), but if weight is an issue, the Matrix's clearly is the better choice.
NOISE
With both channels at maximum volume the Matrix generates some hiss. The Atomic does too although less so.
The fans in the Atomic are much more quiet than the Matrix, you can hardly hear them.
MAINTENANCE
You can't go wrong with the Matrix. As a solid state amp it needs no maintenance.
As where the Atomic will need tubes replaced in time (the front panel bias point is very handy though), which will cost you money. Also, it needs to warm up each time you switch it on and there always the risk of switching it on without a load resulting in damage.
LOUDNESS
The Matrix is a loud amp. I don't think I'll run out of headroom soon when using both channels and 2 12" speakers.
That being said, the Atomic is louder, really much louder. I maxed the level on both and used the Axe's output pot for volume control. I had to turn down the Axe's volume each time I switched from the Matrix to the Atomic in order to prevent ruining my ears.
The Atomic generates (non-controlled) feedback earlier than the Matrix, probably because of its overall Presence (see below). Luckily not nearly as bad as my Reactor powered cabs did when using single-coils....
CONFIGURATION
The Matrix has mono (parallel), stereo and bridged modes.
The Atomic has two separate channels, which cannot be bridged, but you can use them simultaneously of course.
With the Axe-Fx these differences don't really make a difference.
The Atomic also has 4 speaker outputs (Matrix: 2) and other handy stuff: ground lift switches, impedance switches, and Throughs for the inputs.
PRICE
Here in Europe the Matrix is substantially cheaper than the Atomic.
TONE
Well, finally: tone.
First, I've enjoyed the Matrix a lot since getting it. The switch from FR to power amp+guitar cabs (loaded with EVM 12Ls) restored punch and simplicity in my setup. There's no urgent reason for me to change that. And the Matrix gets raving reviews from a lot of other players too. I will not hesitate to recommend it to anyone seeking an affordable, very portable solution.
Compared one on one, I like the Atomic's tone even better. Where the Matrix is quite flat, I feel that notes jump out of the Atomic more, it's 3D, it has dynamics. The Matrix is a bit gritty (can't think of a better word), while the notes from the Atomic are more round and natural.
There's also quite a big difference in the Presence / mid-highs area. The Atomic is more clear and transparant, has much more top end. Note that I kept its Presence control fully CCW all the time (which is "flat" acc. to the manual). And this (top end) makes a difference. For example I have an Uberschall preset that sounds a bit "hollow" through the Matrix and needs additional eq-ing to cut. It immediately sounded better and clearer through the Atomic, without eq-ing. The Atomic adds body (not bass) to the tone.
OTOH, the low end on the Matrix seems tighter. I think that presets need to be set up properly to prevent bass notes from getting flubby through the Atomic.
That's it for now. IMHO both amps are great and winners. It just depends on your needs, requirements and budget.
I may add stuff to this review, or edit it for improvements/clarifications, if I discover new stuff. I won't do recordings or videos.