Jerkass Woobie: Maxwell Madison, Jr. He's one of the bad guys, and pretty creepy as well, but it's still easy to feel sorry for him. When you consider that Rebecca raised him, you realize he has a valid Freudian Excuse if anyone does.
Moral Event Horizon: "The Gauntlet" reveals that Rebecca regularly has homeless people kidnapped for experiments, and that so far all of the abductees have died with the exception of Sparks's parents, who have been forcibly converted into wetware for Project Gauntlet. Sparks is forced to kill what's left of them to destroy the system and end their suffering.
Narm: Sparks asking, "Is the Phantom's dad really going to do the maximum terminate program?" Especially bad since the show almost never used Never Say "Die".
Seasonal Rot: In what is possibly one of the quickest onsets of this trope ever, the latter half of Season 2 is noticeably more episodic and less well-written than the rest of the series. The series finale in particular feels rushed and incomplete. This was caused initially by Executive Meddling trying to make the show more accessible to children, then by the show's production staff learning that cancellation was imminent, causing them to scramble to give the series a proper ending. Despite this, many still consider the series to have been too good to last overall, and at least it got a proper ending. That's a lot more than can be said for many other series that faced similar circumstances.
The jetpack biots. God-flapjacks-dammit, they constantly and endlessly swarm you whenever you're in a map where biots are the local grunts. And they are in 70% of the available maps!
On a minor note, the mini drones. Unlike the example above, who flies in, fires either a single shot or a salvo, and then goes away, the mini drones will NOT let go of you until destroyed. To make things worse, their hitbox is as small as they are, which makes hitting them an exercise in frustration, and their color scheme blends in with a lot of the backgrounds available, so you probably won't notice one nearby until they open fire. Luckily they're kind of a rare sight. They can also be defeated with Homing Missiles — which can only be acquired by defeating the boss of Chapter 3, who uses three of those drones at all times to attack the player!
No Problem with Licensed Games: This series got an even more obscure (partly due to being released very close to the launch of the next console generation) video game for the SNES and Sega Genesis. It's a Metroidvania shooter with plenty of weapons, with emphasis on the use of a Grappling-Hook Pistol. There's a lot of areas and subareas to explore, and a branching plot with Multiple Endings. A great but obscure game for both systems. Even if you don't know the series, you owe it to yourself to try it.