1st of all, thanks for the contribution in advance
yes, it would be better to keep the diffuse alpha for its alpha, and use a separated specmap on 3rd skin (could be combined with a glow map). 2nd normal+height is fine. actually I modified the standard shaders due to it for myself.
probably deferred rendering is a good target, as it has a lot of advantages.

what I use or would like to use, and should work together smoothly (when I use the default 3dgs shaders, as I try a new one I always find another with which it cannot be used together):

- pssm shadows, supporting alpha texture self shadows (mainly needed for vegetation) - with clipped or fading out far shadows (tweakable parameters for performance/quality)
- (maybe another simple shadowmapping option would be fine too for some cases)
- nice water shader featuring reflection/refraction with foam and depth, with adjustable wave size, direction and speed
- terrain shaders, a simple blending 8 textures, and maybe another one supporting normal+specmap too. fading tiled textures to average color on distance would be great (to eliminate bricky texture look).
- a flexible normal+specular+height+glow+teamcolor mapping,
- vegetation wind animation shader - working without shadow offsets or other issues - with tewakable parameters (height of anim start, speed, amplitude)
- pp: hdr, bloom, color correction, (but there are existing solutions for them)

hehh. it is too much.