As mentioned in the description of Sonic 3, Sonic and Knuckles was the first (and last) Mega Drive game to feature a lock-on cartridge that other games could be 'locked into' for added features and the like.
I liked the fact that you didn't have to have different selections for the left trigger because it was always your lock-on missiles.
The right trigger fired your primary selected weapon and the left trigger fired your lock-on missiles.
Luckily, the crosshair will 'lock-on' to a close enemy so you're not over-compensating the target.
There's no sort of lock-on system, so it's all about aiming, which isn't the easiest thing to do.