Lets say I have 2 species such as humans and ponies. They have different skeletal systems so the uniform bone array will have to be different for each species. Do I have to
You can use n-by-1-Textures as a replacement for arrays. Texture size can be specified at run-time. I use this approach for passing an arbitrary number of lights to my shaders. I'm surprised how fast it runs despite the many loops and branches. For an example see the polygon.f shader file in the jogl3.glsl.nontransp in the jReality sources.
uniform sampler2D sys_globalLights;
uniform int sys_numGlobalDirLights;
uniform int sys_numGlobalPointLights;
uniform int sys_numGlobalSpotLights;
...
int lightTexSize = sys_numGlobalDirLights*3+sys_numGlobalPointLights*3+sys_numGlobalSpotLights*5;
for(int i = 0; i < numDir; i++){
vec4 dir = texture(sys_globalLights, vec2((3*i+1+0.5)/lightTexSize, 0));
...