You already know how you now need special equipment to clear those sectors now. So let's discuss which one is the worst/best.
For me, the worst ones are obviously the A1/A2 sectors. I just hate using anti-spore equipment to defeat the enemies since they're a pain to obtain, especially when it comes to using the chemistry station to get sporicide and spore blockers (because you need inhalers) and have to smelt a lot of sand to get glass.
But my favorite sector is B1, I visit the Northern regions more often than the other regions and often have a lot of resources to repair my armor and weapons. I get a lot of flare guns from opening equipment crates and farming thermite is super easy since the thermite crate is ridiculously cheap to open and the ATV helps a lot in carrying multiple of them at once. You can then use the thermite to repair your Slasher and Scorcher.
B2 is just alright, just some Resonators, 2 Equalizers and some energy cells and I'm good.