I'll chime in as I do own both amps.
Personally, I think both amps can be set to sound great and are very cool!
Okay, now that I got that out of the way, I will now provide my pros and cons of both amps:
Atma Pros:
1. 3 channel footswitchable amp (okay more like 2-1/2 channel footswitchable amp because tone controls are shared on Ch2 & Ch3) offering a nice clean, crunch and lead high gain sound.
2. The Atma offers some nice clean to semi-clean sounds in Ch1 that can be set to sound really nice, but only offers a single "tone/gain" control and a 3 position bright toggle switch for tone shaping.
3. Channel 2 & 3 offer a 60's, 70's and 80's mode setting which drastically changes the sound of the amp based on the era.
4. All 3 channels offer an independent volume knob.
5. Ch2 & 3 can be set to sound nearly identical for the given "Era Mode" selected (i.e. 60, 70 or 80's), but at different volumes since they have independent volume knobs, but more importantly the amount of gain in Ch2 can be scaled back from Ch3 gain (by an adjustable knob in the back of the amp). Honestly, without this awesome feature, I wouldn't consider Ch2 & Ch3 much different at all.
I usually set Ch2 gain (located at the back of the amp about noon or slightly higher). Ch2 gain setting wide open equals the amount of gain set for Ch3 in the front of the amp. In other words, the gain setting of Ch2 can never be set higher than wherever the gain setting is at in the front of the amp for Ch3, but can be dialed back.
6. The Atma has a good sounding effects loop without sucking a lot of tone.
7. Power watt setting of 18, 5 and 1, although all 3 channels are set to whatever is selected.
8. Modern / Vintage switch located in the back of the amp that has a HUGE impact in tone, feel and volume of all 3 channels regardless of setting. I put this in the "Pros" because it makes such a big difference based on setting. That said, I much prefer the "Modern" voicing most of the time because "Vintage" adds tons of volume and not better sounds for my needs with my guitar / cab.
9. Easy access to tubes for maintenance when necessary. Simply unscrew the four screws and you have easy access to all tubes / components. I am not an amp tech, but do appreciate the easy access to the tubes.
Atma Cons:
1. No Standby Switch! This might seem to be a non factor to some, but it is my biggest disappointment of the amp. I HATE the pop that I hear when powering off the amp to switch guitars.
2. Limited flexibility in Ch1 for clean sounds. It basically offers a single tone/gain knob, Ch1 volume knob and a 3 position dark, medium, bright toggle switch to shape you clean sound. The good news is that I really like the clean sound offerings from Ch1 with the bright toggle switch selected to bright, but only then! I haven't found good clean sounds with bright switch set to dark or medium.
3. Multiple power settings of 18, 5 or 1w are universal to the amp. At 18w....this amp is surprisingly LOUD even through a 112 cab. Even set to 5w mode this thing is loud. This isn't necessarily a bad thing, but when you set the amp to Vintage mode instead of Modern mode.....it is MUCH louder at 18w or 5w. Kind of backwards of what I thought. Lastly, the 1w mode is whisper quite. Huge difference between volume levels while set at 5w vs 1w. I was actually somewhat surprised by this compared to other amps that I have owned that offered 5w and 1w power settings.
4. There is no built in reverb. This isn't a big deal to me, but I do feel that a built in reverb would be a nice touch.....especially for the "clean sounds" in Ch1.
5. There is a huge volume difference between the 60s, 70s and 80 mode offerings of Ch2 & 3. This in itself isn't a problem because each channel has a dedicated volume knob. That said, don't be fooled by thinking you can have your gain, treble, middle, bass knobs set and then manually switch between 60's, 70's, 80's mode of Ch2 & 3 because all things equal.....you could be in for a deafening surprise......especially in 18w mode, but even 5w mode.
Mark V, 25w Pros:
1. Standby mode offered! Hurray!
2. Independent gain, treble, middle, bass, presence controls on both footswitchable channels.
3. 3 selectable modes in each channel (but not footswitchable) for either channel
4. All 6 modes offered can be set to sound fantastic with different guitars / cabs / personal preferences.
5. Optional footswitchable Graphic EQ in both Channels. Not a requirement, but offers an incredible palette of additional tonal options or can alternately be set more as a volume boost if desired.
6. Nice sounding built in reverb circuit with independent control for each channel (not footswitchable, but defeatable by turning it fully CCW in either or both channels)
7. 10w/25w power mode can be set independently for each channel. Makes a big difference in tone, feel and volume, but 10w can still be set to sound fairly loud if desired.
8. Cabclone feature included which allows for silent recording, direct plug-in to PA system, headphone use for silent listening.
9. Nice sounding effects loop without significant tone suck.
Mark V, 25w Cons:
1. Access to replacing preamp tubes REQUIRES removal of amp from Chassis period! I don't care how small your hands are......this is required. That said, I have had incredible reliability from my Mesa Amps in the past so this will not likely need to be done very often. It is certainly not going to be easy for those that love to "tube roll". I personally do not....so not a problem for me.
2. Personally, I have been able to achieve excellent sounds for all 6 modes on the amp (yes, this is a pro). That said, I am in love with the clean sound offerings in Ch1 AND the Crunch mode of Ch1! The problem is that I can't footswitch between my most awesome clean sounds and the awesome crunch sounds in Ch1. However, it is a small sacrifice considering that awesome crunch/lead sounds are also offered in Ch2. Especially when engaging the footswitchable GEQ set to taste!
My preference is the Mark V Mini, but I truly think that Atma is also a cool amp that can be set to sound fantastic too.....just not as versatile for my needs as the Mark V Mini!