One of best mods imho for SS, faction and ships are cool, but mods which actually adds new mission types are rare.
Also I have suggestion, how can Base Defense mission might be improved "lore wise", they are cool from gameplay perspective, but kinda looks strange common sense wise, like station commander waits for you in bar, and if you don't accept it nothing happens, I have idea for that how to make them more "logical" - give them not via bar dialog, but same way as vanilla random bounties and scan object missions are given, via intel when you flying around sector, and if player interested he just fly to mentioned in intel planet and use bar dialog as "timeskip" which spawns fleet immediately, and if player ignores, simply spawn fleet which will attack station, to remove situation where world just waits for player to something happen. Also they aren't invading planets, they just destroy station and leave - you can change mission description like they just going to raid planet, and as failure create some random shortage of wares and disrupt some buildings. Also another suggestion for them, change how bounty paid, right now these missions pay much - give some small money for participation and rest of bounty pay per destroyed ships, like vanilla system bounty works, also another optional option, random attacking factions are fun, but for "lore" I might suggest optional option which will pickup only fleets of enemy faction of station owner, with pirates maybe as backup, for potentional situation where faction have no enemies at all.
As for other suggestion, more mission types always fun, also another idea since mod missions pay much more, change vanilla ones to make them pay more, also maybe add "special" bounties against various [REDACTED] including Omega, change vanilla ones, like add random situations to scan missions like Pather Fleet patrolling research station and such, so they aren't just free money without risk you can do on single Dram and so on, make vanilla missions pay on par with mod missions and such. Also another idea is Gate eruption, basically bounty which requires to scan specific gate, and once scanned, some [SUPER REDACTED] fleet flies from it.
