I like the Castle of the Two Sisters because it has so much character, the old, crumbling ceiling, the traps, secret rooms, etc. It has it all
When the Castle of Two Sisters was inhabited, I'm betting that Celestia never told new staff or guards where the traps were.
Canterlot Castle is much cozier and well-stocked, but if I'd thought about it for a second longer, I would've voted for the Castle of the Two sisters. There are tons of traps, secret passages, and mysteries yet to be discovered.