Yeah, mazes sucked. But they've had the right idea. I personally think that a game with one of the best level design I have ever played was the original System Shock (oh the shock!) it seemed that what they basically did was to design a space station, and then put some roadblocks around - many of which were avoidable via secret passages or you just got numerous directions that you could have taken. It was fantastic.
Other game I mostly liked was Duke Nukem 3D. It did have some maze crap and the button puzzles were utterly horrible, but you often got cities designed in a fairly logical manner, which allowed for exploration and some degree of freedom of movement. Same applies to Blood in most cases.
The only modern FPS games that seem beleivable in the way that levels are constructed are STALKER games, and perhaps Bioshock to some extent. Everything else is just plain weird - blocks of buildings where you only can enter a single door, entire city where a single road is free, etc.