It's not only about software..
Think that Quartus is for Altera, whereas ISE is for Xilinx.
FPGA advantage is a general sw for all vendors, but I've never used it and I don't know how you can use the IP of proprietary chips (in first approach I don't think it's possible also because IP usually use also proprietary functions of FPGA).
In my opinion I prefer Altera over Xilinx expecially because ISE imo is very poor compared to Quartus.
Quartus is very easy to use and fully integrated whereas ISE seems to be a collection of sw that exchange between themself big files.
Told that if you like FPGA Advantage and inside it you can use the IP of Altera use it (but I'm not sure you can), else Quartus is the way.