As the game has shifted to making protecting Havens from attack the main concern of the player, two issues have arisen, or perhaps simply became more apparent.
The game turns into an endless grind of protecting Havens from attack. The only way to do this is through tactical missions; there are no strategic options to improve Havens’ capacity to defend themselves. The purpose of these missions (both Haven defense and attacking Pandoran bases) is not really to win, but to avoid losing, and thus you end up spending most of you time doing something that doesn’t advance the game.
The Havens lack individuality, character, something to distinguish them from each other, or to assign them comparative value. Or put another way, there is little reason to consider any Haven more important than another, despite them having different populations and facilities that create synergies between them (for example, the Haven with a good production facility produces food for itself and for nearby Havens, the Haven with a military training facility contributes to the defense of other Havens, and the same thing happens with manufacturing).
What I propose is to utilize the game systems that already exist to create a stronger Haven ecosystem. This would reduce the number of Haven defense missions the player has to do by switching the objective from protecting each individual Haven to protecting the Haven ecosystem.
To this end I would:
organize most of the Havens of each Faction into 3-4 “clusters”, so that the player would have to keep track of 12-16 clusters, rather than 80+ Havens.
ensure that within each cluster there are Havens specializing in at least defense and food production (but in some also manufacturing and research)
boost the impact of having specialized facilities (so, for example, the military training facility would give a much larger boost to defense of the Haven itself and others in the same cluster)
The idea is that these clusters can take care of themselves more often, and the player has to intervene less, like when for example Pandorans attack simultaneously several Havens in the cluster and the Haven specializing in defense can’t come to the rescue of the food producing Haven.