I though of a new weapon for the crafts: the EMP Cannon. You need to research New Fighter Transporter to Unlock the EMP cannon. The EMP Cannon is manufactured in the workshop, requiring 25 Elerium and $275,000 for the weapon and has a limit of 9 shots, recharged for free. The EMP Cannon is a unique weapon, has a rather short range but always hits and does nearly as much damage as the fusion ball launcher, 200 to be exact. Also, the EMP cannon will never completely destroy a UFO, not even the smallest one as it is used to disrupt electronics of the craft. Any UFO downed by an EMP cannon is more likely to be intact as the only real damage is from the crash, and thus, you'll find more resources and more live aliens.