i read both paragraphs pretty much twice or three times so i can build a good comment on it.
Pirates and aliens should have planets. We could make OGame a lot more complex, there could be multiple alien nations and pirate factions going in and out of war with one another that would be able to make basic agreements with human alliances, but it doesn't really need to be that complicated. I'm thinking of a very basic sort of AI that has a few planets, builds up its mines over time, has a 90% predictable online/offline/fleetsave schedule, and launches probes and attacks on any targets that seem profitable - and a pirate's profit margins could be extremely narrow! Pirate empires could pop up in particular neighbourhoods and become a menace - or a good source of farming. They could pop up anywhere - the GOs could run them in a macro sort of way, deciding to put 15 pirate planets off in the middle of Galaxy 7 and see if anyone moves in to stop them from getting too powerful. Players in a particular area might have to cooperate in order to put the pirates down, you might have a weaker player telling a stronger one "hey, pirates are attacking me from their moon here, so their fleet should be returning at this time, you can blind phalanx them and maybe pay me for the info", etc, etc. Inactive planets that are due to be deleted could be taken over by pirates instead. Aliens might operate on a completely different ethic, two tribes could be warring with one another with such a rage that they don't even pick up their own massive debris fields...
pirates and aliens idea is pretty much really interesting idea on my side, i really love how you thought of it and developed the idea etc..
but on pirates side:
if they need to attack etc... as you said the profit marge should be high considering their fleet and pirate ranking ( weak pirate, medium or powerful etc... ) so that they dont do a big harm for everyone.
also, automated players like pirates, cant actually watch activity and safety probe and stuff like that, it just a probe and launch for them, coz u cant make them learn about the human intelligence of watching activity and if there was activity predict whether its a probe that created that, transport mission, actual player onlined or overviewed. .., re-watch when activity disappears again etc...
so by this you lose the intelligence factor for pirates in attacks... so it will be really easy to actually ninja pirates etc...
about alines, yeah, why not, first come first serve bases about who gets the df, nothing to say about that

( BUT the df should be in a certain marge between like 400k resources and 3kk resources )
Stars could occasionally go supernova (but miraculously reforming somehow ;p), giving a 7 day warning, which would destroy all fleet around all planets in a given system in a single instant - requiring players to move their fleets away or to be in the middle of a fleetsave for that moment. Perhaps players would somehow be able to CAUSE these supernovas in another system... deliver 1kk deut to a sun? That would simplify a graviton crash! The real cost of solar satellite energy would be driven up generally if everyone knew that regardless of whether or not they were attacked, they would have to rebuild their satellites eventually. Minor (unpredictable?) solar flares could either cause solar energy production to shut down or skyrocket for a short period of time, triggering a flurry of graviton attempts!
thats a NO for me for different reason:
graviton is the ultimate research to do, and making it easy isnt really a clever option
also, causing supernova by a simple 1kk deut is something bad, i can drive someone to put his fleet at the end near my planet or moon by causing supernova everywhere he has a moon except the one near me and hit him.
this can be abused somehow ( cant explain how exactly, but it can )
so, a no for this part for me
Expeditions could be enhanced - the sixteenth slot could actually have its own debris field that everyone could see, destroying a pirate/alien fleet could actually provide some benefit. Fleets lost 'to a black hole' could actually re-emerge somewhere else (slot 16) - unpiloted, ready for another player to see (scan) and capture (send 2 LC to capture 1 unpiloted one, for example) and the player who lost their fleet to a black hole would be the first to know where it went. Droid colonies could be discovered, providing a short term production boost to one of the mines on the planet from which the expedition was sent. Wormholes with short lifespans could open up in pairs in different slot 16s across the universe, suddenly shrinking the distance between two places (distance calculating here would be quite complicated, also how to specify to a fleet that it goes through this wormhole and comes back before it closes etc, but it could be worked out)
this could be abused for pushing.
in my opinion, that will lead into pushing, when someone wants to quit, he is lower ranked, he send his fleet on 20-30 parts few parts of his fleet will get lost in black whole, he knows where they will appear, and tells a higher ranked player ( that is his friend that they will appear there, and he goes for it ) and by that it isnt resource pushing by getting unfair resources, but its a ship pushing ( in my opinion ), could be abused and not a practical system to work with.
and if GOs should watch these things, means more work for GOs which are understaffed in ALL communities, so more job, not enough GOs, and GOs have personal life, so not practical
Each system could have an asteroid field between planet slots 4 and 5 (that's what we have here in Sol anyways) each with 7 different asteroids that could be captured (requires the continual stationing of a colony ship) and mined. Example; you target an asteroid (4:237:4,5c) and scan it: 1.439.776 metal, 814.113 crystal and 11.929 deuterium, no mines or solar plants, 64 fields. So you capture it with a colony ship and a few truckloads of res and then decide what to build on it. (The colony ship is sacrificed when you capture the asteroid) To the right of your 'planets' column you have an 'asteroid' column. Let's say that each 3 levels of astrophysics lets you mine 1 additional asteroid, and you can automatically occupy one asteroid without any expedition tech. For this asteroid specifically, it probably would not be worth the effort to build a deuterium mine. And it wouldn't necessarily be beneficial to build the metal or crystal mines too high, since youll lose them eventually - they should be just high enough that you can farm it in a reasonable amount of time, without worrying that someone else will just capture it, but not so high that your profits from the asteroid are actually lowered by the input cost. While you mine it, the metal/crystal/deut remaining on the asteroid diminishes. Because an empty asteroid might actually be valuable to a player as a place to launch a fleet from, they are only destroyed when the player decides to destroy them. If an asteroid is left undefended, it can be captured by another player's fleet - and they would get all of the mines that have already been built on them, and 100% of the resources that have already been mined and are ready to ship! Shipyards and robotics factories would be the only FACILITIES that could be constructed on an asteroid, but defenses could not be built. When an asteroid is destroyed, a new one takes its place 48 hours later. Another possibility is that the asteroids aren't actually mined with buildings, but with Colony ships themselves, which land on the asteroid with their little mini colonies for a set number of hours (taking up an expedition slot!?) and pull out a set number of metal/crystal/deut per hour per colony ship (a rate adjustable by further research into... say... ion and plasma technologies?!)
not sure about this idea, too much complicated and needs much more further studying.
and about how comets works and behave and how to catch them... it is way too complicated to be programed and coded in my opinion, too much details to get it.
also, players will have to go through tons of calculations and maths, and use deut for the ships, so eventually, they get a small df of 400k or so.
sorry for the long post again

also, welcome to the origin board