Coming up with something new for research could be great, but I think the trouble people have with a mini-game is that it feels separate from the rest of the game. Instead, maybe try to come up with something that ties into the game even more, like getting research by capturing locations, or by holding onto certain locations over time. Maybe different locations give bonuses to different types of research. This could be done in a way that simplifies research, or in a way that adds another dimension to it.
Also, I agree that the first time playing, I want research to be a discovery. Sometimes with 4x games, they feel to me like they're not designed for your first playthrough. With the very first research you pick, it makes me want to understand the branches of research that follow, overwhelming me with too much information all at once. Research in XCom felt like a good discovery, researching different types of alien tech, having an idea of what you might get from it, but not really being sure unless you've played before or looked it up.
In my game, there are exactly 3 things that you can do. 1: throw your army against your opponents. 2: negotiate with your opponents. 3: research new technologies which give you leverage in negotiations, war, and have their own end goal where you get on a space ship and leave.
*Update: I'm not sure I totally understand your game, but maybe research would be boosted by either winning a fight or by successfully negotiating (resulting in a boost for both sides). So instead of research being it's own separate game, you might succeed in research by making good decisions of when to have war or peace without fully committing to one or the other.