Long story short, the good outweighs the bad.
The core gameplay mechanics are good, however there are some major issues concerning the lighting system. The game constantly breaks the laws of physics, with shadows showing through concrete floors and other unbelievable phenomenon throughout. The AI are usually quite competent, however they will occasionally stand there doing nothing or run in to walls for no apparent reason. Levels are large, with many hidden secrets to discover, which makes the game feel rewarding and interesting.
The only major issue with Area-51 is the poorly designed multiplayer mode. Too often will players be spawned right in the midst of a firefight, with nothing to defend themselves other than a pistol.
I really enjoy Area-51, so I find it a bit disappointing that it is so unappreciated.
I understand it's not in any way revolutionary or groundbreaking, yet I feel it still deserves more attention.