These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Anvilicious: The evil enemy council is veryObviously Evil, and extremely anvilicious about how all would-be tyrants are fundamentally the same. (It includes representatives from almost everyone who was in power under the old system, regardless of country or ideology — including both a Dirty CommunistGeneral Ripper and a capitalist Corrupt Corporate Executive who wants to nuke civilization back to the stone age because the modern post-scarcity economy is too equal, for instance.)
Puma + Cloak + Flamer = You win. Always. Simply drive up to the oil rigs, decloak for a quick burn, then recloak and run like hell. The enemy can no longer fight back except for defense. The flames will persist and consume the rig eventually, even if you don't do much initial damage. It works in almost every mission except the last one. It can be done before you get the flamer, too, but you're more likely to lose the Puma since there's no damage over time. Even when the enemy respawns them, you just need to fly a plane over as a spotter, then rinse and repeat. In the rare cases where the Puma's built-in firepower isn't enough (some missions stick a bunch of turrets around to discourage this), the fact that it's completely undetectable unless it moves too close to an enemy unit makes the Puma a perfect spotter for Antaeus' guns. This can make some of the more difficult missions (especially the second to last one, where the enemy are dug in hard and you're on a time limit) much, much easier.
In the final mission, the Vulture gets a massive damage bonus with the Warhammer, enough that five shots will demolish any construction facility. This is supposedly balanced by the fact that it has armor like paper mache and no slots for soulcatcher pilots (they'd botch it anyway). However, the Vulture becomes almost completely invulnerable if you simply point straight up and accelerate, sending your plane so high up that no AA can target it and almost no enemies can see it. Then just fly over the factories, bomb them out of existence, and go back for the turrets. Easy life. You will have to fly back down on occasion to shake off fighters that follow you up there, but it doesn't take long.
Hell Is That Noise: The hellish chitter-whirr-animal noise the Species units and buildings constantly emit. On the other hand it makes them very easy to detect, even if they aren't appearing on your radar.
Nightmare Fuel: The disassembler, nanomachines reprogrammed to rip a target apart from the atomic level. Your normal Grey Goo scenario just makes more nanomachines. This one leaves behind a blood-red puddle of goo and a melted landscape. And then there's the sound. Just watch.
There are repeated mentions that a disassembler attack turns humans into protein sludge. That means the aftermath could be harvested for food.
That One Level: In the level where you go to the real Island Zero; if your first wave fails to cause crippling damage to the bugs' main production facilities, it becomes almost impossible for you to collect enough energy to clean the island. But the bugs have no similar problems.
Also the isthmus mission. Recycle everything. Create a wave straddling the isthmus. Inch forward. Create carnage, a little bit at a time. Advance to protect the recycling units. Use almost all the recycled bits to replace thrashed units. Repeat oh, maybe a dozen times. Then hope there's enough energy left for your main assault.
The escort mission is your first taste of the Species arbitrarily growing new units even if you've cleared the entire map. This in itself wouldn't be so bad, but the mission also forces you to waste two slots on static attack platforms and the final assault takes place on an isolated corner of the map surrounded by AA. You're pretty much guaranteed to lose your aircraft if you don't see it coming, and even then they might get themselves killed.