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Plasma Cannon: 85% hit chance, 100 range, 800 dmg on easy + normal, 700 on classic + impossible. 48 armour penetration on easy + normal, 33 armour penetration on classic + impossible
EMP Cannon: 100% hit chance, 85 range, 1200 damage all difficulties, 44 armour penetration all difficulties
Armour penetration just results in more damage, as far as I'm aware it doesn't affect the chance of components being damaged, seeing as EMP cannons have higher penetration and leave stuff intact.
The good thing about EMP cannon is that it does not damage ship components, so you don't get any damaged UFO flight computers or power sources. Damaged components are only good for being sold on the gray market, while unbroken ones can be used in research and sold for a higher price too.
While EMP cannon does do more damage and has a higher chance to hit, you'll spend about 2 extra seconds getting closer to the enemy ship before you can use it, where you would have gotten 1 or 2 Plasma cannon shots off.
If you're playing easy or normal, it doesn't really matter which you choose, the game's easy enough to win even without extra stuff from UFOs.
on classic or impossible it could make a difference if you're low on resources, the EMP cannon is more expensive but you'll be getting more UFO components and things like weapon fragments + alien alloys to make up for the cost. Also if the ship is not damaged, I believe there tends to be more aliens on board, but I could be wrong about that. If I'm not though, more enemies also means more loot.
You don't actually need the cores to build the Fusion Lance, you only need 1 to research it.
EDIT: You also get early fusion cores with the Slingshot DLC if memory serves.
battleships first appear on the 6th month, but it is possible to get one earlier if you have the Slingshot DLC and you have done the Gangplank mission, where you raid an alien battleship.
the battleship should be along presently.
Alloy u only get from intact UFO parts, so yes, more of that too....