a mode that lets you run up AIP willy-nilly seems to cut out the heart of that decision making. So, what are the trade-offs, here?
Massive exowaves.
I've kind of gotten that, but if it doesn't require careful selection of what systems you take (and my sense had been that this calculation was gone, but correct me if I'm wrong) then what difficult decisions are there to be made, really?
First off, if you move too fast with the campaign, you will probably be crushed. Exowaves at the start come fast. They slow down as you progress, but get even harder as they do. By the time you construct the first city, you may well be facing multiple dire guardians as a result, and you haven't gotten more than 4 frigates yet. (One spawns the instant you start each city)
These waves don't start from one place either. I've seen them start from at least 5 different locations at the same time. In order to properly defend yourself, you are going to have to choose worlds where you can A: build your cities to level 2 and B: not introduce too many more avenues of entry to your space. Failing to do this will leave the waves knocking on the door to your home, with you spread too thin to stop them from entering.
Not all spire city structures are as useless in combat as others.
The colony hub, once constructed, is nigh invulnerable, but serves no other purpose but to allow you to construct other parts.
Shipyards increase your ship cap, carry a beam cannon like every other module, but have no capacity for modules.
Reactors and Habitation centers carry 7 module slots, one for a heavy weapon/shield, 2 for medium weapons, and 4 for smaller weapons. They also have a beam cannon themselves. Spire shields are 25 million/56 million/86 million hitpoints, quite large, semi hard (enemies cannot pass, but they do not reduce damage of protected structures/ships) and heavily overlap the area where the hub is. If you place the hub near a critical defense point, it can provide many hp of defense as well as give many more guns to it's defense fixed to that location. Losing these modules does not interfere with your spire fleet, or shipyards elsewhere once built, so long as you do not have to rebuild a shipyard.
Spire Galactic Capitol is a 7th module for a city somewhere. It carries the same heavy beam all other modules have. It is useless for you once you complete the final scan and have everything unlocked you want for your fleet. You can have it in harms way as a result for more firepower.
Taking all of the above into account, and that reactors work for shipyards anywhere, there is nothing stopping you from picking 2 city locations on the map and building a spire city which will eventually have a hub, hab center, and 5 shipyards because the AI will never bother it, while 2 other locations have a hub, hab center, and 5 reactors to bolster static defenses through a choke point or protect a critical structure. The 5th city (assuming you stop at 5) will have to be a regularly built city. Remember once you build a city, it doesn't have to stay configured how you built it. You can scrap structures if you feel you need the added ships now, but want the better defense later on.
To get the Mk II spire shields you need to unlock MkIII shields, which gives you even more defensive options. To unlock the rail cannons MkII and MkIII you need to simply unlock spider turrets. To Unlock MkII plasma bombs you just need to unlock Plasma Siege Starships MkII. Laser modules require similar Laser turret unlocks. Shield MkIII, Plasma Bomb MkIII, and one more I can't remember, not only require the corresponding Human tech upgrades, but further research done at the galactic Capitol. MkIII rails and MkIII lasers however do not. (MkIII rails require the shield slot on your city. Your call)
Taking all of this into account, thought process on taking systems does change, but doesn't go away. It's less about "What systems can I take for the most benefit to reach the level I need to defeat the AI" and more "Where could I place another Spire city without having to open my borders too much. Where can I place one where it won't be targeted by the AI. How can I design my entries such that a spire city can slowdown/stall/prevent access to a key structure" This kind of planning is paramount as once a city hub is placed, it cannot be moved until you can produce your own colony ships.
