TA3D's major problem was probably its pathfinding algorithm which did not meet the needs of such a RTS engine. Units could get stuck or take strange paths and there was no interaction between units which means two units colliding could stay stuck until they refresh their path which takes a few seconds to prevent flooding the engine with pathfinding requests.
A new Pathfinding engine
This is history. TA3D now has a new pathfinding engine designed for multi-core CPUs (but it'll also run on single core machines, TA3D can still run on low-end/old machines). This new engine is based on minimizing an energy that is computed from terrain slope and obstacles (units, trees, buildings). It produces paths which tends not to get too close from obstacles which results in units not being stuck.
This new engine uses this same energy map to detect units proximity and when a unit is idle in the way of an other unit it just lets it pass. This gives interesting behavior. Now units don't get stuck any more in massive groups of units unable to find a way out because there is no way out. If there is no way out of the group other units will let you pass. Think of it as a kind of fluid with fluid particles being the units.
I've posted a small video showing the new pathfinding engine in action with a factory building units which automatically go away to create some space for newly built units.