But why do you ever need other games when you have Perpetuum?

Must be Nians again, sneaky bastards

Could be. There's some ways to do really interesting PvPvE activities. But it should blend togther in truly interesting way, not just by removing Alpha protection from farming and mining or by simple reward multiplier.
One of very successful examples were wormholes in eve, with a lot of unique group PvE and PvP gameplay. Looking for "adventures and fortune", not for artificial "PvP fun".
But potato

Remove PvP and most of the problems will dissapear.

I know that most of you oldfags want the PvE completely removed, totally same as in eve.

But the fact is, potential new players are often asking about PvE, and will they'll be able to play it if they aren't all in PvP.
So if choosing exclusevely between PvE and PvP, reasonable choise is PvE. In terms of marketing and player retention.

Less content is bad

More content is good

Specialized bot for nexus modules might be a good idea.
Something like command ships in eve. Bonuses to nexus, low damage, and very good tanking capabilities.

You can get some better balance by doing more missions

Tiers are fine, add sizes.