jtag pin voltage levels

a) according to the Altera schematic, the AS connector should use 3.3V at pin 4, the JTAG connector 2.5 V.

b) The serial flash parts are supporting 2.7V to 3.3V according to the datasheet. If you don't want to introduce another supply voltage level, the EPCS supply voltage must be 3.3V.

The unclear point in the Altera documents is about the expected configuration bank voltage with 3.3 V EPCS supply. According to the I/O standard matrix in the Cyclone IV device handbook, you won't use 2.5V VCCIO. Personally, I have used 3.3V config bank voltage up to now. I omit a separate AS programming interface since several years and use indirect JTAG programming instead.

If 2.5V VCCIO should be used throughout the design, I would go for 2.5V serial flash. As far as I understand, the new 2.3 to 3.6V types are basically software compatible to existing EPCS like industry standard types, but don't expose the old style signature byte. It would be interesting to know, if someone has used a 2.5V serial flash sucessfully with Quartus programming tools and Altera FPGA.