You might have enabled emulate 3 button mouse in File → User preferences → Input. This causes left alt + left mouse to be interpreted as a middle mouse button action. Either disable this option or you might try the right alt button (although that might not work on all keyboard layouts / operating systems)
For leaves the simplest way is to create your leaves in a particle system on an object in a separate .blend file and link or append this particle system to the file that contains your tree. After this the new particle system should be available in the particle settings drop down in the particles tab of the leaves object (this is an object parent to the tree skeleton and separate from the trunk object as well). When you click Update tree the appropriate number of leaves will be set.
Any material can be applied to the mesh that represents the bark. The mesh is uv-unwrapped, see technical details section on which uv-maps and vertex color layers are available.
No. Although it shares the same algorithm to generate the branches the resulting tree object is different.
Interactively drawing lots of branches and leaves requires a decent video card. Performance tends to be less dependent on the CPU. NewGrowth should work with any video card that is supported by Blender but to get a decent performance a GTX 970 or better is recommended.