Gene's directive of where the bridge is kept, I guess that was a retention from naval vessels. The bridge is generally at the top, looking over the rest of the ship.
It makes sense from a story standpoint because the camera can zoom to the bridge, and then you can fade to the bridge set (as was famously done in the original pilot).
Also, tactically speaking, why go after the bridge anyway? Just for the emotional punch of killing the captain? If Picard and the bridge crew get taken out, it's not as if the other 1,000 people on the ship would just surrender. Pretty sure everyone from LaForge in engineering to Ensign Ricky in stellar cartography would continue to fight.
It makes sense if the purpose was to raid the ship. With no captain or chain of command, the rest of the crew would be confused and easily defeated if there was an invasion.