I am curious as to why the Federation Dreadnought which cannot be used or claimed until you reach Vice Admiral comes with all Captain-level weapons and systems? And why is the photonic lance not a console system but the cloak is?

Because it used to be a RA ship and they forgot to change over the weapons from VIII to X when they made it a VA ship.

Also, it is a phaser lance and it is not a console because it would make no sense seeing as it is integrated into the visuals of the ship.

I thought I remembered that you could get it before VA...I wouldn't have bought it if it was something you couldn't use. I think I remember the top of the command chain used to end at Rear Admiral.

Well, that's lame, they should be able to fix this little mistake pretty quickly.