Some of the armors and weapons make sense for the upgrade system, the Tac Vest being needed for the Tac line of armors makes sense, each one is just a normal vest with more pieces added to it.
Maybe what we need is the option to skip the upgrade side completely, and just use the base materials to make the selected end item, along with the capacity to hide project options in order to keep the clutter down. We do that right, and it doesn't matter as much about the project bloat, since you can just hide the ones you don't currently care about.
So still able to upgrade normally, with the capacity to just build the end project if you have the resources ready, would probably take the same amount of time, just less micromanagement, and the capacity to hide projects you don't want to see