Unfortunately, this is a limitation of the Glest engine. The AI has problems with size 3+ units, since their pathfinding ends up horrid and AI don't usually space buildings far enough apart. And I can't make units smaller because not only does that make telling the difference between them very difficult, but they are already at their smallest size. Finally, most maps aren't made with very large units taken into consideration, and when experimenting once, I ended up crashing glest a lot due to insufficient space on many maps (of course, that was just an experiment with far larger than practical units). And of course, another problem is that units that are "long" or "wide" more than they are "tall" would end up taking up too much space if made to be a suitable size vertically. It's like the transport ship, for example, which is the largest size for a moving unit, being a size 5 (which is more than crowded enough already, and naval units are largely limited to maps made with naval units in mind), is still looking awkward in comparison, since to make it "to scale", it'd have to be at least size 50!
This is a common limitation in RTS's and TBS's (take the civilization series for example), but has no current workaround.
As an update, it's getting there, but I've been *very* busy with work, school, and a bushload of homework, so that set it back quite a bit. I hope to finish the next version before christmas, and then we can get started on the "cult" (which, by the way, I am still accepting opinions, ideas, and concepts for it. I want to hear what you want!).