As the game is right now, and with how many different stats, the game is getting more and more complex and difficult to balance. I think something allowing players to be more free with how they play should be priority, and the current tuning tree/nodes system is very restrictive in that sense.
I think we should have something similar to a skill point system instead of tuning trees and nodes, where every mission gives skill points on its first completion at that difficulty level. This allows the player to choose which stats they want to maximize without restriction or forcing the player to play a certain way. For example, what if I wanted to be a tanky Revenant? Unfortunately the Revenant architect sacrifices most of its defense. This would allow Tank Revenant to become possible, and would be easier to understand for some players.
Special abilities like all of the subnodes in Architect can still be trees and equipped on the build, just organized into relevant subsections and maybe some requiring a certain amount of points in certain stats to unlock.