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LRS is something I will always pay for up to sector 5 and always sell at the last store in sector 7.
Drone recovery arm is great, sell in sector 7, you will have enough parts for mothership by then.
Stealth weapons is fantastic (paired) in the end.
Preignighter is good, but sell in sector 7, not very usefull in the end...
Scrap arms are GREAT! Sell them off in sector 7.
Maybe we should hijack the op and ask what to ride 1-7 with and what to end with. I'll take a scrambler, steath, and reloader to the flagship.
Long-Ranged Scanners - Helps you get better beacons, especially in nebulae.
Automated Re-loader - Lower cooldown can mean taking down their weapons before they hit you, or could mean out-DPSing the Flagship.
Rock Plating - With the Flagship fight being more of a DPS race now, having ~18% more effective HP can actually be pretty relevant. (Also saves about 20 scrap over a run.)
Backup DNA Bank - A bit of a luxury, but cheap enough to be a good insurance policy.
Shield Charge Booster - I'd say Shields and Shield Recharge are a bit stronger in AE; I'm reasonably happy to have one of these, though it's hard to quantify exactly how helpful it is in practice.
Scrap Recovery Arm - Going to pay for itself if you get it by Sector 4, though the opportunity cost of losing that 50 scrap in the present is very relevant on Hard.
Zoltan Shield Bypass - Good with certain boarding setups; often doesn't make much difference.
Fire Suppression - Usefulness depends on the ship layout and crew (it puts out fire at the same rate a Mantis would, but puts out all fires simultaneously). Really pricey to justify buying, but can be somewhat decent.
Mantis Pheromones - Quicker movement speed allows for more effective kiting strategies when boarding and getting around your ship faster is somewhat useful; fine to keep or sell.
Distraction Buoys - Very similar to Scrap Arm but worse (costs 5 more, doesn't work right away, requires fuel).
Engi Med-bot Dispersal - Mostly a luxury, but can be nice to have especially early.
Stealth Weapons - Very situational, and even in the good cases generally not terribly exciting.
FTL Jammer - Less silly now with how fast enemies can jump away on hard, but still doesn't have enough effect to actually be desireable.
Defense Scrambler - Does useful work, but costs a ton (even keeping a free one costs you 40). Rarely quite good situationally.
Explosive Replicator - Missile weapons still suck, you won't generally be using 2 bomb weapons, and pricey at 60 (you need to fire 20 missiles to break even, which isn't hard to hit but if you're hitting it easily you're still running out of missiles anyway). Occasionally decent, often worthless.
Emergency Respirators - Not particularly exciting, but does let you board Auto-Drones more reasonably and helps fighting off Lanius boarders. Especially worth keeping for a while on the Fed. C.
Slug Repair Gel - Another luxury item - repairing breaches is nice, but 30 scrap early is often more important.
Reconstructive Teleport - I still don't understand why I should be excited about this: expensive, the loss of combat skill from being cloned is only 1, and similar effects can be gained from upgrading Medbay and Teleporters.
Titanium System Casing - The purpose of this augment is to be sold to help you buy Shields. Often worth keeping on a Shieldless run though.
Battery Charger - Too expensive for what it does: your batteries are still down for 10 seconds.
Lifeform Scanner - Does offer a few useful blue options, but 40 is a lot to play just to try and force Mind Control to be more useful when there's so many other strong Systems you could be getting instead.
Hacking Stun - I can construct scenarios where this is great, but those are so ridiculously specific I don't really know that I'd ever actually use it in reality.
Repair Arm - Drains a whopping 15% of your scrap for 2 repair and costs a hefty 50 initially to boot. Stores are not rare enough the incremental heals are helpful and you will lose scrap in the long term. Has some small utility by giving you 4 extra health against the Flagship.
Adv. FTL Navigation - Even worse in AE now that Last Stand repair stations cannot be re-used. Would need to either not advance the Rebels or allow connecting to previously seen beacons to be of any use.
Drone Reactor Booster - At least the Engi B starts with this piece of garbage for the free scrap? I don't understand why the speed boost isn't at least 50%, or even 100% (same speed as normal crew).
Almost absolutely perfect analysis. Specifically, that if you have ever, ever sold Zoltan Shields for any reason, you are objectively insane.
My only disagreement is on the Backup DNA Bank. I find this fantastic when playing a clone boarding strategy. I'll note that since I'm substantially less skilled than you, I more often end up in situations where a bunch of my crew are in the clone bay when it gets hit.
(I'll also note that another solution to this is to max the clone bay so one of those stupid 2 damage Artemis missiles that apparently every ♥♥♥♥♥♥♥ rebel in the galaxy has can't take it out in one hit.)
Also, I'd note that another reason Crystal Vengeance should be in "sell this garbage immediately" is that in addition to being 40 free scrap, this augment's main purpose is to kill your entire boarding crew at random 10 percent of the time the enemy ship hits you at the last moment when you're playing some edgy combo of boarding and shooting off weapons.
Crystal Vengeance is not even an augment. It's a gun aimed at your own foot, waiting to go off at any moment. Get rid of this horrible thing, and not just for the free scrap.
ETA: Also, I'd have a special tier for Drone Reactor Booster. A "why does this ♥♥♥♥ even exist" tier.
For a while I had Repair Arm in its own, bottom tier because it offended me just how awful it is with the high amount of scrap it steals from you. However then I realized while you generally want to sell it off if you're gifted one for free so it stops robbing you, the late-game utility of 4 extra health can actually be useful in maybe 1 in 100 games, which is more than I can say for the Reactor Booster or Adv. FTL Nav...