Yeah, I found the Quick Hack , Breaching, Stealth all levelled up fairly smoothly.
Well, when I say fairly smoothly, I had them around 16-18 after that 104 hours of my first playthrough.
Handguns and Blades were around 14-15, whilst my Athletics was incredibly draggy and I think was just hovering at 8 or 9.
Having a proper pause from the game now, letting things settle, my memory haze a touch, and what patches might turn up in the next month before properly getting into a second play.