Interfacing microcontroller with 1.8V logic
NXP has 74 different Cortex-M0 controllers, so if the M0's performance is good enough (they run at 50 MHz maximum), then you'll probably find a type which has the right features for your application.  

If you want more options or need a higher performance you could go for the Cortex-M3 combined with a GTL2000.



The GTL2000 offers you 22 fast channels which you can use unidirectional or bidirectional, and as you can see in the diagram you can interface with several voltage levels with a single device. The GTL2000 can work with levels between 1 V and 5 V on either side. This is a cost-effective solution if you have many lines between the controller and FPGA, but there are also versions with less transceivers if you can do with less. The GTL2010 is a 10-channel version.