It's do-able with other systems too. D&D the RPG wouldn't be my first choice on it, the skirmish game would be a better venture.
Speaking of other systems.... Chaos in Carpathia or Cairo would work. They have the random scenarios similar to Mordheim, which you could alter or use as a series of linked scenarios. I'm sure there are other games played by folks on the forum that are similar. The other big advantage would be the Fate points, and the Mook or Henchmen rules.
If you are looking at each player having three models per side, it can become a one sided match quickly, if some lucky dice rolling offs a character. Fate points mitigate this to a point. It also gives the game more of a pulpy feel, which I enjoy. Now I know you mentioned three models per side, but say a scenario had a say group of angry natives, or civilians. The Henchmen rules are a great way of presenting cannon fodder types, I'd just consider removing the Fate rules from them.