stefaan,
If you really want to have your ISR at the irq entry point there is nothing stopping you re-writing the code which lives there. This can be found in the nios2 component in the file alt_irq_entry.S. Though obviously the hal APIs to do with registerring interrupts will no longer work.
As for you comment about it the old SDK that it would be useful if the memory map was separated from the function prototypes, structure definitions etc. This is something we completely agree with. This is why with the Hal you will find that system.h does not contain structures, function prototypes etc, and only contains information about the hardware, it's memory map etc. However I should say once again there is little point requesting new features on the SDK it is included for backwards compatability, but there is no new development scheduled for it.