Well what You are saying is correct
The amount of help is inversely proportional to the amount of freedom
For this reason I hate the engines which make too much for you
A typical example was Torque which was geared towards FPS multiplayer games
However we should not make also the opposite mistake
I went through some absurd threads on GameDev forum where fanatic programmers supported by even more fanatic moderators claimed that game engines are of no use
A game programmer should code everything from the scratch ( direct x or opengl ) in the name of flexibility
About 3dgs and Unity3d in my opinion they are the right compromise
These engines supply just those features which are in common to all games
Features which the developer should in any case code by himself
Templates and prefabricated scripts are options
Dont use them if you dont like them