First off... Well it's Alpha so I shouldn't be too worried about forking over my 100$... or should i... I'd be worried if there was no additional substance beyond better graphics. Anyway these are just my opinions and I'm far from an expert so here we go.
1) Technology
A) Technology should be a strategy game in itself, but with the capacity to have a clear defined path to your technology goals. Setting up a queue will help move the game along a little faster. Perhaps interjections when tech is stolen, discovered or acquired by trade.
Reverse engineering as a way randomly extracting tech (or failure to) from 1) Precursor relics discovered 2) from captured enemy ships or planets As far as planets go what even is left over from the invasion can be used, but it's shouldn't mean you're allowed to just start constructing it on other worlds without any research effort or other type of cost. (destroying object in the process)
C) Prototype design templates for specific ship building. I like to build a specific type of ship with a specific set of systems, but I would like a list of specific research techs required to produce that ship. I found that galciv 2 was not always intuitive when i wanted to construct a specific ship. Selecting specific templates in order of priority will show a research queue that can be imported to your active queue might be cool... (this would be very handy for mods based on Star Trek/Wars, B5 etc..
D) Overrides to specific weapons and defenses may help as well so that you can adapt to the enemy. I think a version of that was included in galciv2... Very handy tool.
E) Combining different tech trees to access special technologies (whether race specific or precursor)
2) Combat
Maybe a couple things I would love to see. I think space and planetary combat should be realtime for every encounter, but with the choice for auto resolving before and during. So perhaps 3 options before the start of combat (Auto Resolve, Cinematic and Tactical Control. The tactical element is one of the most exciting elements. Perhaps some technology that gives you the probabilities of the outcome before you choose to assume command or auto resolution.
Starbases attached to your planets
3) Civil
Ability to transfer population automatically to lower pop growth planets with dedicated transports (operate like the trade routes of Galciv2)
60$ is for an amazing game... 100$ deserves nothing less than epic. It's just a quick bunch of ideas.