If you already own NIOS I and speed isn't an issue then stick with it.
However, NIOS II is smaller, faster, and it's not too bad for programming (I'm a hardware guy and I have very little problems programming on NIOS II, mind you I don't do complicated stuff like OS programming).
If you have neither core take NIOS II because of the advantages (that and the assembly language of NIOS I is already obsolute so an upgrade to something else like NIOS II, or NIOS III (if it comes to that) if they did do ASM code they would have legacy problems).