This guide will help people realize when to let go of certain ships, buildings, assets, plans, or strategies when a new one is available; with certainty of knowing you won't have to go back ever unless specified in this guide or required by a mission or a friend.
Transporting ressources with ships manually: you could set up a very large supply chain for a few minutes then cancel it (or setup a permanent one) instead of wait possibly several hours/days for stuff to move. This is rather useful if your waste is about to cause unhappiness and you need to shove it around other colonies for a while...
buying lesser glyph buildings for every new colony as a new player: these days you'll want to get the best glyph buildings you can get on one world, and set a supply chain to as many colonies as you like. SUPPLY CHAINS ARE MORE CONVENIENT THAN PODS! You may want to buy some legacy berth 1 ships to get it going such as maxxed stat hulks --- don't think of legacy hulks as a 'SPENDING' as you can always sell 'em back at full price once you have better options.
most of your regular ressource buildings: while they're nice and you need some food type variety to keep your people happy, soon you'll have a pond, a geothermal vent, a volcano and a natural spring cover your needs. While harder to level up, you'll need much less regular buildings. A lost city may seem to obsolete them all but it has rather EXTREMELY slow build time, will not level up to 30 without help from a dillon forge, and will cost extreme amounts to repair after an attack so better have some glyph buildings who only require a click to repair to help.
lost city of tyleon: UNLESS you want to make L25 space station plans yourself (in which case the city is good for storage), 4 glyph buildings instead will cover your every ressource need (without costing plots! This is why lost cities are not that optimal on non-gas giants or even low plot count for a gas giant planets!), the food diversity is nice but that will soon be filled instead by excavators when you get lots, the lost city it DOES generate some happiness but with the space/cost you could have more than one junk building generate more, the lost city requires COSTLY repairs instead of a click for glyph buildings so you can't rely on it alone, it does eat waste but you could just have a wastechair with one megascow scoop that out, long term it's not worth leveling to level 30 except for bragging rights... aside from the ONE benefit: it costs you less E! In theory (since its construction times does make many people spend E!) not to mention cost of pieces!!! It's only claim to fame is that you could theorically get a level 29 lost city of tyleon faster than level 30 glyph buildings, but let's do some math here... can you REALLY spend all the ressources a level 25 tyleon or glyph set produces in one day unless you need to upgrade a lost city?? If you REALLY need to make waste for a black hole generator, save yourself 100's of E, just buy the waste 100 million per shipment off the market!!!
missions to gain ressources: mostly obsoleted by glyph building you'll buy, unless you need specific ressource types a mission/bulding requirement has at the time you need it.
Dory: obsolete when you could have a legacy galleon or better (berth=1) instead. In fact, any ship that has less cargo, less speed, and equal or more berth than another you can get easily is obsolete (unless you need the stealth). Dories are however EXPENDABLE if you need to scrap them to make space which is convenient.
Regular ships you can make: you can occasionally get better than player-creatable in missions which you can buy regularly and have a fleet of 'em, or lower berth if you need from legacy ships, there is enough of those to keep your entire empire outfitted if you can afford it until superbulk becomes important and the huge hulk rules.
spy shuttles and pods: relatively obsolete as smuggler ships are reusable and can send many spies you wish to be captured for genetics labs experiments in one go. They'll need to see the target first, tho, unless you know the scripting API.
Park: obsolete compared to anything else, except when your construction times are pathetic due to very negative happiness... then making level 1 parks fast and dumping food into them (no construction slowdown for parties/dumping food in parks) might help. A Kalavian is quicker, but you can only use one...
Kalavian ruins: obsolete compared to any junk buildings; it's good to keep until you need the space since they don't use plots tho. Their only claim to fame is you can build them very fast during a construction slowdown due to *MASSIVE* unhappiness, but you can only use one...
junk buildings except the pyramid: you really only care for the trash pyramid long term, unless any of the lower level ones are 'good enough for now'. You WILL want a junk pyramid on your happiness-specialized world someday if you want to make as many colonies as possible, so might as well start now and never upgrade any other kind of junk building if it can be avoided.
4 basic storage buildings: obsolete compared to a distribution center and/or an interdimentional rift, except for that excruciatingly annoying lack of a 'dump' tab on those. However with the new supply chains feature, this doesn't matter as much as before as you can export ressources to a world who can dump them and recycle (if only to keep your recycling buildings from getting damage from being out of waste). You will need some basic buildings back when upgrading to lost city level 29 but don't keep 'em around just for that yet.
Entertainment districts: obsolete by luxury housing and others, unless you are in a mostly unsettled zone and can with the lottery more than once a year. Really sparse regions will mean hostile AI attacks will concentrate on you tho.
University: obsolete as soon as you made one at level 30, unless you like the happiness and can't be bothered to build something better now... BTW capturing a world with a L30 university doesn't give you L30 instantly.
Your homeworld: aw come on, it's probably only 45 plots! It will take months to black hole it into shape, you'll have moved on to gas giants by then! However your homeworld may be useful to put a black hole generator on, if you plan to stay in that zone. Until then once you get 5 good developed planets with 55+ plots it's sorta redundant.
waste buildings: waste recycling centers are they'll be really, really nice early on for extra ressources, but as the colony needs more and more plots the "moving waste from large old colonies to fresh new colony and recycling it with tons of low level recyclers" method will soon be obsolete and you'll just break even and use few recyclers, and eventually only water reclamators then waste exchangers and finally dumping waste into a nearby star with a waste chain. You'll only ever NEED waste for lowering the happiness of your enemies or firing up black hole generators by then.
large piles of useless plans: NOT all obsolete, just ask a dillon forge owner which one he'd like to buy/exchange for glyphs/fuse as higher level plans and discard the rest (whenever you're abandoning a planet, more 'em there first). Keep a few of everything in cases missions ask for 'em.
genetics labs: useless once you got +30 affinities, and changed your species decription for all time, it's useless..
'the gift': NOT OBSOLETE! That colony ship is no longer an obsolete piece of extremely slow junk! You can keep it to fill a mission, but mostly at some point you'll colonise a planet near one you own so if you can spare one spaceport slot they're good.
"storage alliances": soon you'll get distribution centers who are not as convenient, soon after that you'll have enough random ressources from excavators for covering most needs except space station building and certain lost city missions. Your alliance will trade you the ressources you need at the embassy soon enough if you ask politely anyhow, once your alliance has enough kind long-term players. Plus storage chains are cool if you maintain one storage-only-type colony as a giant distribution center substitute. (wich is what space station builders with colonies to spare could do)
excavator targets: asteroids with low ressource count total simply give less glyphs/ore, unless they happen to have substantial quantities of a specific quantity of glyph/ore that's valuable they're obsolete/inefficient. Some types of glyphs are also very very cheap due to dillon forges coverting huge stacks of plans and you shouldn't target asteroids and planets who make mostly those. If you can't find good asteroids, put a space station on a nearby useless planet so you have a chance at having better asteroids.
food diversity worries: lots of excavators that will randomly bring you some random food, making the problem solved provided you don't spend ALL your food down to zero using all the found food. Also once you get one world with sufficient diversity on its own, you can just set up supply chains and only keep the most efficient food types producers on other colonies.