Roddenberry wanted the Main Bridge moved back to the Saucer on the D so viewers could see it- he felt they needed an identifiable area which could be related to.
Internal security is always problematic- if you drop force fields across corridors to stop an intruder the script will provide him a way to get around them (TNG- 'The Hunted').
Voyager had two Warp Cores, although one was a back up unit. The writers conveniently forgot this when they wanted to add drama to a story.
Problem is if they designed the ships to be well engineered vessels with redundant essential systems them most of the stories told would have no crises.