Sorry, my reply was too condensed.
Flow control in Avalon-MM rinterfaces is an optional feature: slaves or masters may not support it. So, you need to write your slave in such a way that it works properly with a master that does not support flow control.
In particular, I think (but not sure) that the NIOS masters do not support it, that's why you're seeing readyfordata being ignored.
The DMA core does support it, so you may want to test your slave with it.
This has nothing to do with the fact that it's being deprecated, though. It's always been optional.
Avalon-MM isn't going away by a long shot. But Altera has chosen to deprecate the flow control feature in it in favor of adding Avalon-ST interfaces to the components whenever that capability is needed.
Not that I'm actually going to argue with you if you prefer to use MM with flow control instead of ST. :)