Random thoughts that might be useful:
Base your control on regions, which are all controlled from a "regional capital" planet. Planets within a region are all specialists, based on the nature of a planet with some minimal flexibility to change what a planet does. Each planet provides various kinds of 'resource points' which are then controlled from just the capital. From that screen you can upgrade a given planets facilities 'to the next level', but don't force the player to manually decide if they want 'another mine in grid X,Y, a Habitat module, or to upgrade the existing habitat to a mk II version. Just keep in simple: Each planet has 3-4 'slots', a main 'infrastructure' slot, along with modifier slots (advanced waste processors/farming/storage, university/academy, intelligence facility, specific kind of research labs, defence systems, etc)
So rather than jumping between 20 planets at the start, you really have 2 or 3 capitals to worry about, and all your other 'planets' are merely modifiers that feed into your main hub where you make all your choices. The main 'infrastructure' slot can be a choice tree and represent general capacity/production from that planet, while each planet's modifier slot gives you strategic flexibility. Do you take the gamble of not taking up slots of core worlds with defence bonus options, and maximize them for production, while making the rim worlds far less productive, but arm the rim to the teeth as a wall against invasion?
Planets suitable for habitation would become your population and agricultural centres which produce food and workers/crew/scientists, but you have the option to decimate them and turn them into industrial or mining worlds. Planets which are borderline habitable would default to industrial production, with the option to invest into improving them for main habitation. Sub-habitable words become dedicated to mining or science which merely feed resources into the system which are then 'used' on other planets, but require food/population support from the other planets they support.
A single screen can then easily allow the player to make decisions on 10-20 planets at a time, so your 100 world empire is easily managed from just a handful of screens. Add upgrades to your main hub world to allow them to control larger areas
This also gives you lots of design options for how the player can control their economics. Keeping it dead simple and just have planets feed resources to the core hub automatically, or putting it into the hands of the player to design trade routes (Which then become vulnerable points of their empire). Depending on your method of space travel this can be a really awesome mechanic in and of itself.
Maybe trade is done by way of Frank Herbert's Dune universe, where each planet is visited by a massive highliner like ship at scheduled intervals. New highliners are a massive cost, so the player would have to plan routes effectively, and decide if they want small amounts of resources to trickle into the core every turn/tick (where they can be used for your major projects/fleets), or do you use fewer highliners with longer routes which will result in having to go several turns without new resources, but then receive massive stockpiles every few turns?