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Did you determine if it is possible to have bank 3A at 2.5V? I am facing the same issue. I want to use AS config mode and also need almost all available LVDS inputs on the device. The documentation indicates that Vccpgm must be at 3.0 or 3.3V for AS mode, but from what I can see makes no mention of bank 3A Vccio requirements. If bank 3A Vccio must be at 3.3V, I cannot place all the LVDS inputs.
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You should take a look at the information on the pins that are powered
up by VccPGM in
http://www.altera.com/literature/hb/cyclone-v/cv_52007.pdf page 7. Various of the signal pins power up using VccPGM and then when configured, switch to using VCCIO for the Bank that they are in. You might have to provide some form of isolation for the lower voltage devices when the pins are operating at the higher of vccPGM and VCCIO - but this will not be very neat.