I owned both at the same time. I bought the MKIII perhaps 89 or 90. It had a blue marker line on it. In 2000 I bought the Mark IV. I found the MKIII much darker than the IV (more than likely due to the EVM12L mounted in the open combo chassis). The MKIII was awsome for blues style. Not bad when pushed in the lead channel. It held up over the Drummer and Bass. The odd thing about the band I was in, I had preference for Pink Floyd, drummer was all Led Zepplin, and the bass player was a YES fan. Once the combined styles were mixed up into the jumbled mess we called music, we sounded like a Guns and Roses tribute band without vocals. Go figure...
I found the Mark IV to be a more versatile amp. Only the clean channel and the moderate gain channel shared common parametrics with the exception of the treble control. MKIII was sweet running all 6L6, it was awsome with 5881 and EL34. (original mesa tubes were 6L6 paired with EL34). As for the Mark IV, I kept the power tubes for channel 3 set for pentode mode. I did not use channel 2 all that much, but once in a while I will play through all channels and change settings to keep the pots in good shape.
Shortly after selling the MKIII, I felt something was amiss with the MKIV. I missed the bass response of the EV speakers (I sold the MKIII with a satelite EVM12L cab my exwife's uncle made for me). I bought a black label EVM12L and stuffed it into the MKIV. It will fit but not much room for tube access. The reverb tank needs to be forced back into its location. Of course were talking combo amp here. At gig level the EV performed excellent but when at bedroom level a bit prominent on the low end. I reinstalled the C90 and reserved the EV for rebuilding the rectro 412 cab.
I love my MKIV for its tone and versatility. The mounted casters on it makes moving much easier than having to carry it. They are removable for better stability when playing. When I bought the MKV head to go with my 412 cab, I was not impressed. I liked the MKIV much better. That has changed since I retubed the preamp and power secion of the V. I enjoyed the MKIII for as long as I have owned it. The smaller size means it will take up less room in the cargo hold of your vehicle. One smart feature on the MKIV is where the foot petal mounts, on the back which provides protection for the tubes during transit or storage.
I would have to agree with most, the mark III and IV are both great amps. Either will rip your arms out since they weigh about the same, 65 pounds is not that heavy, but having to extend your arm out to carry it feels more like 120lbs. MKIII is a bit more compact and esier to carry than the MKIV. Either way you go, you will have a great quality amp that should last an extremely long time. They are worth the expense when purchased new, and they hold thier value for resale (except for trade in, had a mesa dealer offer $225 for the mkIII for trade-in when I bought the IV, I kept it for use as a satelite system for stereo effects. 23 years of ownership on the MKIII without any issues says enough on longevity, durability - many gigs (change in location where the band would practice). I got some feedback from the person who bought it as a gift for his son. "This is the best amp EVER".