User blog comment:Suparockr/List of Plotholes throughout the series/@comment-1679409-20120729154938/@comment-4953843-20120729162204

we are dealing with alien methods of construction here. we have no idea how long it takes for the keepers to fabricate those incredibly resilient materials the citadel is made of.

the other organics would have their own reconstruction initiatives that may or may not conflict with the keepers' own, potentially wasting time and materials in the process.

and the keepers would have a very different view of priorities than other species.

not to mention bioware was going for an "everything's changed" look especially since the citadel always seemed like an island of calm for everyone during the war.

and the best and simplest explanation to most other questions like this: dev resource limitations. far more implausible to revert to the pre-cerberus citadel look than leaving it damaged until the end or remaking the maps to look damaged but patched up - people would complain even more with the former (nothing changed, they'll say), and devs would invoke resource limitations on the latter.