Okay. Here's how the Eclipse and the Rapier stack up against each other.
Eclipse: Better speeds, on both the ground and the air. The Lightning Gun the Eclipse carries is capable of hitting all targets within a 25 yd radius of wherever you fire it, meaning it's an excellent weapon for taking out groups, whereas the Rapier's Laser Cannon can only fire on 1 target per shot. The Eclipse's Hyperedge Claws/Acid Drip combo also do better damage than the Rapier's Hyperedge Spurs at close range. And actually the Eclipse has a just as many sensors as the Rapier does, though it's Targeting is 1 point less than the Rapier.
Rapier: The Rapier has better stat adjustments to the pilot's characteristics than the Eclipse - boosting Agility by 2 and Perception by 1. The Rapier is also more durable than the Eclipse, its Integrity 10 (compared to Eclipse's Integrity 5) allowing it to take twice as much damage before it expires. And while the Rapier's Laser Cannon doesn't do as much damage as the Eclipse's Lightning Gun, the Laser Cannon holds on longer, having a higher Failure Code - it fails at Critical Damage, whereas the Lightning Gun fails at Medium.
The real question is what you want to do with your mecha. Eclipse is excellent for making hit-and-run attacks, using the Lightning Gun to damage multiple opponents, and then run away so it can set up another ambush. The Rapier, on the other hand, might be able to last in a battle where the Eclipse can't.