Models - dumb opaque boxes

The next step - after providing a terrain - is to put something on it. I was thinking about a few different plants and an animals or two, say elks and wolves. Obviously, I didn't want to draw (or create a models of) all the plants I need. Using just one model doesn't sound good either - who's ever seen a forest of identical trees?! The right approach would be to have a model of a tree with a trunk and a branch, as separate objects, and then randomly choose the height of a tree and number/position of the branches on the trunk, proportionally to the trunk's height.
Turns out, jME considers all models more or less opaque 3D-objects. From code point of view, they are just arrays of bytes (wrapped in Nodes) without any insight into their composition. That makes it impossible to generate a tree at runtime or have any real way of merging models.
Character modeling is in even sorrier state, because this way one needs to draw (make models of) all permutations of armor type-weapon-body type, and that's if I somehow can apply a pattern to a model!
There's got to be a better way of doing things. Let's see what available!