Awesome Music: The entire soundtrack is quite good, but special mention goes to the title screen music, and the final chapter's music. Considering the composers (Hyperduck Soundworks) are the same pair who did Iji's soundtrack, this is not surprising.
Broken Base: Opinions on the Steam release of A.R.E.S. Extinction Agenda EX from fans are divided. There are those that don't mind the changes in EX while many others loathe it. The fact that EX is being sold as a separate game instead of a patch doesn't help.
Goddamned Bats: The Sentry Pods, oh, God. They fire three shots simultaneously, each shot going in a different direction. This can be very annoying when trying to rack up combos... Or even trying to get somewhere, as shown by those two vertical shafts in Stage 4.
Some parts of the chapters have shielded Bombers that you have to bait into crashing into a wall, which isn't too bad, but excruciating if you're going for high combos.
Assault Pods are about as bad for your combos as Sentry Pods, except they shoot in an arc at you.
It's Short, So It Sucks!: A common complaint from the original is its short length and only feature 5 playable stages that can take an afternoon to play through. EX however later added 2 more stages and features a second playable character with their own weapons and abilities.
That One Boss: Chapters 3, 4 and 5's (Chapters 4, 6, and 7 in EX) bosses are all quite hard, but increasingly so. The worst part? To get SS rank for each stage, you need to kill them without taking damage. Trying to get that Genesis Suit is not easy.
Chapter 3 (4 in EX) has the Sentinel, which warps around quite a lot, and it has attacks that literally require you to use the ground dash's invincibility to avoid taking damage.
Chapter 4 (6 in EX) has the Prime Guardian. Its first stage has attacks that are difficult to dodge even when you can see them coming, and then it Turns Red...
The Minos Core/Cannon. There is no achievement for perfecting it, and you can get SS rank without doing so. There is a good reason for this: it's Bullet Hell in a platform game, but primarily the third phase of the fight, which has several long-reaching attacks (the pink and green turrets) and can use multiple at the same time. EX, unfortunately, makes it mandatory to beat said boss for not one, but twoachievements.
That One Level: Chapter 3 in EX features several segments with falling junk that interrupts you in mid-air, likely leading to you falling to your death, that's very difficult to get the timing of. During this chapter, there's a part where you have to air-boost against the junk to get to a timed door. This is before you get the H-Class armor (or Fusion Form for Tarus) and its upgrade that makes you immune to hitstun when air-boosting.
They Changed It, Now It Sucks!: Fans of the original were upset with changes made in EX, such as the simplified mechanics, the redesigns of the female characters (Valkyl was given a more Westernized artstyle, whereas Dr. Carson's EX design made her look less of a scientist and more of an outright Action Girl), and the levels were made easier than the original game.