Okay. I know what's going on and some of how to fix things.

Starting with the upgraded buildings is actually very bad. They have a much higher upkeep - something you can handle later in the game, but not at the start. They also don't work at all due to the player not having any rare resources at the start of the game, resulting in a paralyzed empire. They really don't cost that much, so I strongly suggest rolling them back to the original buildings and districts you start with. Paradoxically, the Crowded Slums blocker is actually a good thing to have a handful of - each time you clear it, you gain a pop.

Also, the other two planets need specific deposits; I think that the homeworld generates properly because the game is told that it's a homeworld, but the other two are empty of anything that's not specifically added. These deposits are added exactly like any other type, but you may want to add multiples of them.

Most of the orbital objects were initiailized with set_deposit - which means that only the last deposit added worked, as it overwrote the others. There appear to be other stacking rules (research + dark matter works, but research + zro doesn't? Confused). The gas giants also had geothermal vents (invalid for that type) which caused them to not produce anything at all.

Here's my best jab at fixing it, if you want to plug it in. I get a weird system name in the star system select but it works in the actual game:

### Arcadia System
arcadia_system_initializer = {
name = "NAME_Arcadia"
class = "rl_all_stars"
asteroid_belt = {
type = rocky_asteroid_belt
radius = 85
}
flags = { empire_home_system Arcadia_system Arcadia}

usage = custom_empire

planet = {
name = "Arcadia"
class = star
orbit_distance = 0
orbit_angle = 1
size = 50
has_ring = no

init_effect = {
prevent_anomaly = yes
clear_deposits = yes
add_deposit = d_physics_10
add_deposit = d_minerals_10
}
}

planet = {
name = "Deuteros"
class = "pc_black_hole"
orbit_distance = 50
orbit_angle = 20
size = 15
has_ring = no

init_effect = {
prevent_anomaly = yes
clear_deposits = yes
add_deposit = d_physics_10
add_deposit = d_alloys_5
add_deposit = d_dark_matter_deposit_3
}
}

planet = {
name = "Lantiell"
class = "pc_asteroid"
orbit_distance = 35
orbit_angle = 160
size = 10
has_ring = no

init_effect = {
prevent_anomaly = yes
clear_deposits = yes
add_deposit = d_minerals_10
add_deposit = d_alloys_5
add_deposit = d_engineering_10
}
}

planet = {
name = "Tilfall"
class = "pc_asteroid"
orbit_distance = 0
orbit_angle = 70
size = 5
has_ring = no

init_effect = {
prevent_anomaly = yes
clear_deposits = yes
add_deposit = d_minerals_10
add_deposit = d_society_10
}
}

planet = {
name = "Oshia"
class = "pc_asteroid"
orbit_distance = 0
orbit_angle = 60
size = 5
has_ring = no

init_effect = {
prevent_anomaly = yes
clear_deposits = yes
add_deposit = d_minerals_10
add_deposit = d_energy_10
}
}

planet = {
name = "Remallta"
class = pc_gaia
orbit_distance = 40
orbit_angle = 250
size = 25
starting_planet = yes
has_ring = no
modifiers = none
deposit_blockers = none
home_planet = yes

init_effect = {
prevent_anomaly = yes
set_capital = yes
clear_deposits = yes
clear_blockers = no
add_district = district_farming
add_district = district_farming
add_district = district_mining
add_district = district_mining
add_district = district_mining
add_district = district_generator
add_district = district_generator
add_district = district_generator

add_deposit = d_submerged_ore_veins
add_deposit = d_fertile_lands
add_deposit = d_geothermal_vent
add_deposit = d_alien_pets_deposit
}

moon = {
name = "Taris"
class = "pc_frozen"
size = 5
orbit_distance = 12
orbit_angle = 40
has_ring = no
}
}

planet = {
name = "Joheil"
class = "pc_gas_giant"
orbit_distance = 30
orbit_angle = 180
size = 30
has_ring = no

init_effect = {
prevent_anomaly = yes
clear_deposits = yes
add_deposit = d_exotic_gases_5

}

moon = {
name = "Entmandus"
class = "pc_toxic"
size = 10
orbit_distance = 12
orbit_angle = 115
has_ring = no
init_effect = {
prevent_anomaly = yes
clear_deposits = yes
add_deposit = d_society_10
}
}

moon = {
name = "Rothkov"
class = "pc_frozen"
size = 6
orbit_distance = 5
orbit_angle = 180
has_ring = no
}
}

planet = {
name = "Zentari"
class = pc_gaia
orbit_distance = 20
orbit_angle = 190
size = 25
has_ring = no
deposit_blockers = none
modifiers = none

init_effect = {
prevent_anomaly = yes
clear_deposits = yes
clear_blockers = no
add_deposit = d_betharian_deposit
add_deposit = d_betharian_deposit
add_deposit = d_submerged_ore_veins
add_deposit = d_fertile_lands
add_deposit = d_great_river
add_deposit = d_geothermal_vent
add_deposit = d_tempestous_mountain
add_deposit = d_tempestous_mountain
add_deposit = d_tempestous_mountain
add_deposit = d_tempestous_mountain
add_deposit = d_alien_pets_deposit
add_deposit = d_frozen_gas_lake
add_deposit = d_fertile_lands
add_deposit = d_fertile_lands
add_deposit = d_great_river
}
}

planet = {
name = "Imalta"
class = "pc_gas_giant"
orbit_distance = 15
orbit_angle = 220
size = 40
has_ring = no

init_effect = {
prevent_anomaly = yes
clear_deposits = yes
add_deposit = d_zro_deposit_3
add_deposit = d_society_10
}

moon = {
name = "Ortynth"
class = "pc_frozen"
size = 6
orbit_distance = 15
orbit_angle = 115
has_ring = no
}
}

planet = {
name = "Ungalla"
class = pc_gaia
orbit_distance = 0
orbit_angle = 120
size = 25
has_ring = no
deposit_blockers = none
modifiers = none

init_effect = {
prevent_anomaly = yes
clear_deposits = yes
clear_blockers = yes
add_deposit = d_submerged_ore_veins
add_deposit = d_fertile_lands
add_deposit = d_fertile_lands
add_deposit = d_fertile_lands
add_deposit = d_tempestous_mountain
add_deposit = d_tempestous_mountain
add_deposit = d_great_river
add_deposit = d_great_river
add_deposit = d_great_river
add_deposit = d_great_river
add_deposit = d_great_river
add_deposit = d_rich_mountain
add_deposit = d_rich_mountain
add_deposit = d_rich_mountain
add_deposit = d_rich_mountain
add_deposit = d_prosperous_mesa
add_deposit = d_prosperous_mesa
add_deposit = d_prosperous_mesa
add_deposit = d_prosperous_mesa
add_deposit = d_alien_pets_deposit
}
}
}
}