Lots of little differences and a few big ones. MW 3rd uses D10's, unlike everything else in the BT universe, so it's harder to mesh with the other systems. Not impossible, though, and some have taken the D10's and applied them to all the game products. AToW uses a 2D6 system in a different fashion from everything else in the BT universe but switching back is easy and mathematically identical in results (MOS 3 is still MOS 3).
Damage works markedly differently. In MW 3rd, you get an impact generated by the weapondamage roll, your MOS and a few other factors which is then compared to a chart to see how much injury was caused. Works better with the hit locations rules - the same impact does different damage depending on where the shot lands. A shot to the head is always more damaging than a shot to the hand. Compare the impact to the location and you've got your Wound Value. In AToW weapons do a set damage that can be modified by a high MOS or any MOS if you use an automatic. Using hit locations changes things up a little giving more detail and the AToW companion gives still more detail. Most of these details are more lethal than unmodified combat. :)
Character generation in MW 3rd is a little complicated. You generate a life path and random events happen within each stage of the character's generation, some good, some bad. Some crippling if you had a solid character you wanted to wind up with. A good GM will mitigate these. You add up the points you got in each category (traits, attributes, skills) and compare them to a chart to see how good your character is, then fine tune using Character points. In AToW, you choose a life path with no random events unless you count the optional ones in AToW Companion and even these are not defined more than whether they were good or bad (added or subtracted XP) then you fine tune with XP. Yep, the same points you'll be earning later to improve your character you get a stock of during creation and they pay for everything. Which means you can also skip the lifepath entirely and go with a points only system.
In general, I personally find AToW to be the better system in terms of realism vs speed and the ability to change the rolling system to the same as all the other products out there makes life much easier.
