I’ll try to layout the process I use. See the images below, as I go through the process.
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I create a tree with limbs - no leaves yet. And I will use a simple plane with a texture with transparency (Top corner of image 1) that I will spread over the basic tree that I have weight painted, to produce the tree in the lower part of image 1.
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So I select the tree in Object Mode and add a particle system. The particle system is “hair” and then I tweak the values for Emmision number, seed and select “Advanced”. Going down the image, I set values for rotation randomness, physics size randomness, and choose the object I will use to replace the “hair”. In this case a plane with the image in first image (top corner). Then set the “Density” using the weight painted vertex group.
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Then I tweak these values until I get something I like (lower part of image1). When happy, I go to the modifiers tab and click convert. This produces all the instances (see last image). To complete the tree, I select all the instances and finally the tree trunk and merge them to create my tree.
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Now using this tree, I create the terrain, weight paint it, apply a new particle system choose the number of trees etc. I want and do the convert. It leaves all the trees as instances spread over the landscape (no merging here) with different sizes and rotation.
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Variations come from different textures on the plane, different tree trunks, emission number values, different seed values etc.
Quite a simple procedure really.
cheers, gryff 
