Non-existent voice acting - the only utterances by NPCs are the same type of gibberish heard from the Covenant in Halo - fortunately, that was intentional. While I can accept the excuse of a low budget, a fully text-delivered plot for a title priced over $10 went by the wayside over ten years ago.
Dated graphics - the game runs on Source; while this was used to good effect in Portal 2, it looks roughly equivalent to the graphics we've seen with Portal 1 - without the excellent art direction. There's an ever-present mist to cover for uninspired and often hideous texture and lighting, with many scenes requiring a significant gamma boost to see the steps in front of you.
Poor sounds - no gun echos, no ambient noises, etc.
Poor AI - Enemies have no concept of cover, exhibit no group behavior, don't apply relative weapon ranges to decision making (shotgun vs sniper at range...), and generally just behave like chickens with their heads cut off.
Awful User Interface - Not that a great UI is industry standard, but the game's UI is absolutely terrible. There are three different sets of skills to level or buy up, and all three of them use entirely different pages to access. Further, the skill system is by default not hot keyed, though with customization can be made so. It still doesn't show which keys bind to which powers, though, so unless you've memorized all 20 of your skills, you're going to be constantly referencing the key bindings for actual in-game usage. Don't forget that the UI doesn't freeze the single-player game, so enjoy being repeatedly shot while accessing a skill.
Cool weapon inventory system. I'd have preferred just one more column in the main section for a second primary weapon; as it is, you can only choose one (for example, one of the sniper rifles OR one of the assault rifles). Other than that, it's definitely a neat idea.
In summary, every game should have a focal point and stick to it - whether it be excellent gameplay (with possible multiplayer extensions), excellent story (of which delivery is an extremely important part), excellent novelty (such as fun puzzles or characters or weapons), or some variant thereof. Unfortunately, E.Y.E: Divine Cybermancy has great aspirations in all of these, but drops the ball in virtually every area that counts, and in doing so fails to deliver any of those great aspirations to the player. It's just too unpolished to be called anything but an abysmally poor release.