Welcome.
1) Does GAE support random animation selection for skills like move, attack, stop? The wiki says it's a MegaGlest feature. Felt strange to me that GAE which is a graphical advancement doesn't support random animation selection for a skill.
It doesn't currently support it, but it's a feature request and hopefully would be implemented in the reasonably forseeable future. As for whether or not you could just copy it from MegaGlest, GAE has quite a few other changes to how skills work (effects, for example). How the implementation works in general is likely more or less valid, but you'd have to take a look at the source codes of each to see. I'm not a programmer, so can't really gauge the difficulty of such a feature.
2) What type of Normal maps does GAE support? I have G3DHack and the tool tip tells me "Bump map". Which leads me to believe a greyscale bump map? Activating it with an actual RGB normal map doesn't do anything. I didn't notice any difference in game either. That being said, is green up or down?
At the moment, just normal maps ("bump maps") and spectacular maps are supported, but there's plans to add support for luminosity maps in the future. Normal maps are't actually grayscale, but rather are chromatic, looking like
the example on this page.
As for how to make such maps, you could "fake" it with the GIMP, per
this guide or make it from a higher detailed model in Blender per
this guide.
3) Is there any support for DDS texture compression? Any future support? Does GAE handle its own mip maps? Is it possible to recompile so that it reads DDS instead of Targas?
Glest doesn't support the DDS format, and no plans to add it because GAE supports the PNG format. Use that instead, as it'll give roughly the same filesize without sacrificing quality (DDS compression is lossly, which means that data is lost with each save, negatively impacting quality on commonly edited files).
4) How are docks made? Reading through the wiki, I only read that a unit may be declared as land, amphibious, or deep water only. Is it possible to declare a unit Shallow water only? Otherwise how are water units produced? I was unable to find anything covering this in the wiki. Conversely, is the meeting point/production rally point restricted to water in this case?
I had a
dock in Apocalyptic Dawn. It was a water unit, but had to be built by a land unit. Thus, it could only possibly be "nearish" the shore or in shallow water. The catch? The AI doesn't currently build them properly. That's a programming shortsight, and can hopefully be fixed in the future. Myself? I made a ton of scenarios that placed a dock for the AI.