which cyclone?

I would agree with you for new designs, go Cyclone V. the 3.3 IO's are still supported but you should have overshoot protection diodes. (which is recommend on all these families)

It's a great part family. Only real problem is the naming convention they used.

Cyclone III will probably be around for awhile, but they are dropping support in quartus soon. So you would be stuck in the current version of Quartus for several years. Since Cyclone IV is on a similar process, I could see them dropping it fairly soon as far as support in Quartus as well. Cyclone V is brand new and will be around for many years yet.

The 10 Families are not out yet, and there are targeting the Arria Family and Stratix Families primarily.

Pete