I know this thread is old but someone might still benefit from the answers, as I too used to struggle with wake-ups until recently.
But now I mostly have success doing the input right after I see my character has stopped moving and is lying flat on the ground. That's the cue in for a wake up attack for me. Sure I don't get it every time, depending on what knocked me down, but it works more often than it fails and that is reliable enough for me.