You have to explain more what you have in mind, what exactly disgusted you, what kind of control over a program code you want. Do you mean something like Irrlicht API, where you just plug in subsystems and build the game from scratch?
http://irrlicht.sourceforge.net/docu/index.html
I do feel nostalgic about that, but again, that's a thing of the past or for one-man team projects. While you can start right away and get to coding and enjoying yourself, your whole team is disabled for indefinite time. How long would it take a programmer to write animation viewer tool, so your animator can import his models and animations to check how they look in the game (which can be ranging from "different" to "horrible lovecraftian mess of moving vertices and bones"). How long would it take a programmer to write functional world editor, with thousands of big and small features like "Importing terrain heightmaps" or "Drop object to the ground"? Particle editor, where you let designer choose what looks best, instead of a programmer changing parameter values and recompiling? Cutscene editor? VR support? Your team would just sit and wait for months and years while you prepare the toolkit.
That's partially what I did for AoD, but there wasn't much choice in 2004, when we started. If you want all of that out of the box, you have to have an existing code architecture. The more features the engine has, the more complex the default architecture becomes. You can't just have an empty main() and add "new ParticleEffectsEditor()" and another million of declarations. Features and subsystems are often intertwined - something needs to be called before the tick, something after. Something needs to be rendered at one layer, something at another. One feature works on platform X, another doesn't. So add the platform layer, ticks, messages, timers, rendering pipeline, thread communications, input handling, plugins, editors etc - and your main() is buried and you have to inject your gameplay code "where you are allowed to". Which is where you start at with UE/Unity. Looks like it's an unavoidable trade-off, Torque was halfway down this road. I would be curious to learn about an engine that combines best of two worlds, but I haven't heard of any like that.