One major problem for using alternate softcores, is that there is no smooth way to do JTAG debugging.
If you are restricted to documented interfaces, the only way to do JTAG debugging, is using TCL scripting. It might be feasible to run a debugger that would create TCL scripts on the fly, invoke a quartus executable, and parse the results. But this is hardly usable and would be extremely slow.
You can implement a JTAG debugger using some already reverse-engineered interfaces. But you still wouldn't be able to run the debugger concurrently with other Altera Jtag tools, such as Signal Tap.
This is too bad. I wonder if Xilinx also has so many undisclosed JTAG aspects.