It was mentioned in a dev letter that they would be adding cooldown times to some skills purchased via. guild marks when they remove the stamina bar. I expect these skills will still be of use but not as auto-attack skills. I doubt Flurry will change at all.

For Pugilist, I would expect Heavy Strike would be the auto-attack skill, with Flurry/Pummel/Light Strike all having to be manually activated as before, with Pummel having a short cooldown timer of maybe a couple of seconds.

My only curiosity is how they'll handle the light slash/stab attacks of the gladiator as they basically do exactly the same but with different kinds of damage. I kind of expect light slash will be the auto-attack since it's the default skill that can't be changed. I don't see them going to the effort to give the option to have auto-attack as a skill that you might not even have on your bar as it would over-complicate things.

Ideally, to give more freedom to the players' play style, they should have one slot on the skill bar that is dedicated to auto-attack and it would just spam whatever skill is in that slot for you. This would allow for optional auto-attack even for range attackers.