Why was DOOM 3 such a horrible game? The general consensus from everything I've heard is simple: DOOM 3 is a poor imitation of the FPSes present at its release date.
Though accurate, I have a different take: Classic DOOM (read: DOOM, DOOM 2, and any associated level packs/source ports/etc.) is not the kind of game it pioneered. In fact, let's get crazy here: Classic DOOM has more in common with Super Mario World than Half Life, Halo, Call of Duty, and other modern shooters.
Think about it for a moment: what is Classic DOOM is all about? Your character is a crazy-armed space marine (un)officially called Doomguy. Doomguy runs faster than Sonic the freakin' Hedgehog via use of a run button (Mario), grabs lots of little collectibles building towards a bigger reward (Mario), fights hordes of enemies assisted by precisely zero AI (Mario), and has abilities and tools tuned very well to the challenges he must face (Mario, and many classic NES titles like Castlevania). Hell, the original DOOM's first three episodes have world maps (Mario), and all of Classic DOOM has loads of secrets, both for extra collectibles (Mario) and secret levels (Mario). Classic DOOM isn't even actually 3D: objects cannot share the same X, Y coordinates and rooms cannot exist on top of rooms. Classic DOOM is a Super Mario World variant and, given the kind of game modern id Software strives to make, may well have been an accident.
DOOM 3 is id's attempt to take the kind of game Classic DOOM spawned (read: Half Life) and plug it into a DOOM formula. It is nothing like the original two, and beyond its cons as a "modern FPS" it fails to truly recognize its heritage and how to build upon it. Classic DOOM asks you to use Doomguy's insane speed and huge backpack/ammo clip to weave around enemy shots, run around enemies you either aren't equipped for or don't want to waste resources fighting, tag everything else as best you can, find secrets for power and pride, and traverse through levels only vaguely resembling real human structures. Its mechanics held satisfying depth and worked beautifully, rewarding players who understand the underlying game engine with super-accurate chaingun rounds (the first two shots are as accurate as the pistol, so squeeze and let go in rapid succession), enemy manipulation (you CAN make two Barons of Hell fight each other; get them to claw swipe one another), even faster movement (Google it), totally unrealistic but crazy practical BFG usage (your character is ground zero and only enemies you're looking at are hit with the "aftershock"), real intel on what enemies are truly the most dangerous in open areas sans cover (it's enemies that use bullets, like the various zombies and Spider Masterminds), and more.
I played DOOM 3 expecting a modern take on those classic mechanics. What I found was a tech demo, crafted by people who fail to understand what once made id Software's flagship series truly remarkable. You can find Classic DOOM levels, mods, and editors to this very day, and for good reason.
Classic DOOM has very little in common with the kind of game developers sought to turn it into, and sadly very few devs seem to realize its carefully controlled, thoughtful mayhem. Not to belittle Half Life and its ilk, but all of them built on the Classic DOOM template… and all became something very different. Nothing inherently wrong with that, but DOOM 3 could have been a fresh coat of paint on classic mechanics. It tried and failed to one-up its wildly different descendants instead.
Even if DOOM 3 was the Half Life killer id Software envisioned, even if it garnered critical acclaim, it wouldn't have been building upon its roots, other than aesthetically. Speaking of which: Classic DOOM's cartoonish ghouls, pixelated textures, and bitchin' DOS music are head and shoulders above DOOM 3's.
I truly hope, but doubt, that DOOM 4 will be this dream DOOM game, with Classic DOOM's mechanics, aesthetics, and heart thoughtfully updated and improved.