OK, the real world difference.
MT has 16 load point vs E6X having 32
MT injection time resolution is 0.06ms vs Haltech at 0.008ms. This is a bigger and bigger issue the larger you go with injector, or the smaller the motor is.
MT has 3D fuel maps (they call it Matrix Mode), but 2D ignition rpm with 2D MAP correction. Not true 3D. Haltech is true 3D
MT has a pretty handset so it is quick to make changes. Haltech is laptop only.
MT is locked for your ignition type, meaning you cant eg. switch from a Nissan to a Mazda. Haltech is user configurable.
MT you cant save and load maps.
MT is cheaper.
MT has a few things Haltech doesnt (but should), like MAP based throttle pumps, and throttle pump ignition advance.
MT comes with 20psi MAP sensor on board. Costs extra to go 30psi.
MT only calibrates closed throttle, not full range.
MT comes pre-configured so the car will start and run as soon as you wire it.
MT staged injection has rpm and load selection
MT does not fully do idle control, boost control, or closed loop. It does basic forms, but not very well at all.
Lots more little stuff.
Draw your own conclusions. For me, the ignition mapping and injection time resolution is the biggest issue. Try something like 850cc injectors on a 2L 4-cyl, and with MT you can pick between 10:1 and 16:1 for mixtures. Do it on a Haltech/Motec/Autronic and you can pick the mixture you want, and get it repeatedly. I had a 20B the other day with 6x1600cc injectors with an LTX12 trying to run it. I had the same issue at idle, 10.3:1 and fouling the plugs, or 15:1 and stalling from too lean. I have done 12A's with even old E6A Haltechs that have idled smooth on 1600 injectors at my selected mixture. I had to instruct the owner to run a smaller set of primary injectors. I am not saying MT is bad, it just has limitations that some applications will be fine with, and others will show up as bad with. I have had an LTX8 on a stock standard 13BT pass full EPA emissions tests here, but I have had a race prepped 13B ported, T04, custom intake, big injectors, etc... pass the same test much much easier with an E6K.
For me, the extra small amount of money is worth spending on a Haltech, but if you are on a total budget an MT can get you going reasonably well. They are not the bee's knee's, but they are probably the best of the busget systems IMHO. Just because Racer Joe uses MT does not make it any better a system than it really is.... something the kids on the forums are blinded by.