The libraries that seem suitable:

  - libSDL (2d video output and screen operations, cross-platform, high-level, pretty fast, doesn't use hardware acceleration. probably will only be used for setting up the initial screen and changing resolution, not for the rendering)
  - OpenGL (3d rendering, broadly supported, low-level, needs a lot of work, can be used by intermediate higher-level libs)
  - Irrlicht Engine (both 2d and 3d through OpenGL, cross-platform, small size, sophisticated, easy to use, transparent, functionality, different language backends, pretty customizable, has a lot of different bindings/wrappers - PhysX, Bullet, ODE, anything)
  - Blender Game Engine (known to be nice and shiny, compatible, pretty easy, OpenAL sound, Bullet integration, python scripting, uses OpenGL)
  - OGRE (fairly popular and supported, multi-platform, highly modular, custom shaders support, scripting, visual effects, different language backends. not an all-in-one solution, mostly graphics, no physics, no audio, everything has to be taken from elsewhere or coded as a plugin)
  - Crystal Space (3d framework, very portable, can use (optionally) OpenGL, SDL, X11, SVGALib, assembler code via NASM and MMX, very modular, support for ODE and Bullet)
  - ClanLib (cross-platform, uses OpenGL or a software renderer, can play sound via Vorbis or MikMod, has collision detection, GUIs, XML, networking classes built-in)
  - Allegro (cross-platform, portable, very functional out-of-the-box, has a lot of different language bindings, only limited software-rendered 3d though)
  - Cube 2 (mostly FPS-oriented, quake-like, multi-platform, uses OpenGL and SDL, out-of-the-box in-game level editor)
  - LÖVE 2D (awesome, lua scripting, easy, transparent, very high-level, but only 2d)
  - Glest (a complete RTS game, moddable to suit needs)
  - various small language-specific libraries:
    - python (pygame)
    - ruby   (rubygame, gosu, chingu)
    - etc was too slacky to search

The theme is probably a simulation of scriptable/programmable/customizable entities/creatures/ninjas devouring and deceiving/adapting and taking over/flipping out and killing stuff. Perhaps.
The more decent ideas proposed:
  - cyberpunk (AIs, viruses, antiviruses, rogue bots, something related to network security, the web as a battlefield, bots can take over machines, hide, steal, slaughter and overwrite code)
  - low-level biologic warfare (basically cell biology because I am a fanatic of it. viruses (this time the real ones), mischievous bacteria, genetic algorithms (genetic modifications), some kind of adaptability-based evolution, player-selected evolutional traits, phagocytosis, cell compartment management, player-controlled life support)

The story depends on the chosen theme and can be written later.

Opinions wanted to expand this.