Game Breaker: The Cybran Soul Ripper II. Each is highly mobile and airborne, yet holds as much firepower as a Cybrannasaurus Rex and better anti-air than an Airnomo. They take a while to build, but get five or ten, and nothing short of a fighter Zerg Rush will bring them down.
Tear Jerker: Thalia's ending. She gets arrested and incarcerated for her crimes despite not having known what she was getting into, her brother has died of his illness and she is last seen breaking down at his grave. The game leaves it ambiguous whether her situation will ever get better from there.
They Changed It, Now It Sucks: The sequel did away with much of the economic complexity, added a research element while greatly reducing the unit variety, and has significantly weaker graphics than the original or Forged Alliance. Maps are also much smaller.
Arguably, however, it has strangely better balance and more strategic depth, but time will tell on if this is a successful formula.
The changes were apparently what Chris Taylor was aiming for. Somehow, he wanted to avoid the game devolving into an "Economic Crisis Simulator with Robots."
Specifically he felt disappointed that T1 units were simply being thrown to the meat grinder when the jump to T2 was made and so on. Thus upgrading units seemed to be the ideal solution to stopping it. As for being an 'Economic Crisis Simulator with Robots', part of the enjoyment of the first game was maintaining an energy surplus, while balancing every single unit of metal being produced and feeding it into production. The designers seem to have missed how crucial this is to keep it from being another Starcraft clone. That said, there have been some who criticized the economics system as distracting too much from the actual fighting at times.
The graphics bit was explained as an indirect reaction to the economic crisis and for attracting a wider audience. Chris Taylor apparently reasoned that as not every player owns top-of-the-line equipment and that no one's planning to buy anytime soon, he'd might as well make it more accessible.
That One Level: The first mission in the Cybran campaign, which features an absolutely ridiculous difficulty spike with no corresponding increase in tech level. To elaborate, the moment the mission begins, you're swarmed from three sides by never-ending waves of units. Point-defense towers won't shoot the artillery sent in said waves half the time. You have almost no mass generation to speak of unless you reclaim units, which is complicated by constant waves of reinforcements. And that's just the first half. For the second half, you have to manage to escape before the enemy Zerg Rushes you into oblivion with a mass of experimental air units, gunships, and ground forces that will utterly overwhelm your defenses unless you've turtled like crazy. Worse still, one of the achievements requires you to wait long enough to shoot down nine experimentals.
Win Back the Crowd: The developers released major patches that modified aspects of the gameplay, in part to placate the more hardcore fans of the original game. The end result was an overall better rounded product that appealed to the Broken Base.