I'm still learning about them all. They have differences, but it's also easy to hear the family resemblence working from the Mark 1 to the Mark 4. In fact it's easier to understand the Mark 4 I think if you've used earlier Mark series amps.
The Mark 1 is super punchy and a really nice clean channel, and the lead channel is Santana all day long. Probably the closest Mark to "hot rodded fender" sound, although my experience with real Fender's is pretty limited. The Mark 1 can get flubby bass-wise though, so I find it works best not to dime anything, and use a good boost pedal to really get the lead channel singing. Sustain and Musical feedback are super easy with this amp. It's not a multiple channel amp, so I set it up to have a decent level of saturation than I can then dial back with the volume or hit with a boost. Its an outstanding amp run clean in the low gain imput as well.
The IIC+ I just got, but so far it seems to be more responsive to pick attack, volume, etc, than any other Mesa I've tried. Backing off the volume of the guitar seems to clean up nice without thinning out as much on this amp. It definately gets that Petrucci vibe going on. I find that with this amp I can set it up with a very hot distortion for heavy sounds, and dialing back the guitar volume works very well to bring it back to hard rock land. I'm not yet convinced that the IIC+ is the end all be all of the Mark series, but its a very nice amp with a great lead tone.
I owned a 4 a couple years ago but sold it. I never could figure out R2 on it. I decided to get another M4 and try again, and I think because I've had experience with the Mark 1 and my LoneStar that R2 makes more sense to me now. Super versatile amp. I've got R1 set clean of course. R2 is set to basically work like I use my Lonestars drive channel. Its set for a "hard rock" level of gain that I can dial back with the guitar vol. Hitting R2 with a boost gives a great lead tone. I have the lead channel setup so that without the EQ it gives me a lead channel that is boosted over the other channels, and the natural midrange cuts through nicely. The EQ is setup in a typical V, but brought down as well so that the sound level is equal with the other rhythm channels. So, I can basically use R1 clean, R2 "rock" rhythm or boosted for leads, Lead channel+EQ for heavy rhythm, or Lead Channel alone for solo. Works great with alot of versatility.
Overall, I think the M4 is a bit smoother sounding than the IIC+, but I may not have the IIC+ setup quite right yet. I think the IIC+ can actually get a heavier sound than the 4, but the 4 is close. At the moment my favorite lead tone on the Marks is the Mark IV R2 with a boost.