So for me, the critical issue to separate the autonomous students from the rest would be to specify the strokes to be used; no more dog-paddling, just free, breast and/or side stroke (hey, if you can do fly, by all means) performed to a decent standard: You don't have to be a competitive swimmer, just obviously know what you're doing. And no use of fins, as I believe PADI allows as an option; just you and the water (swimsuits optional

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Boost the swim distance and breath-hold (not done at all in my OW class) a bit to ensure reasonable condition, and/or impose a reasonable time limit on the first; except for students who are already marginal on the first two, I doubt much is proved by extending the length of the float/tread beyond 10 or 15 minutes. If they can go that long they can almost certainly go for 30, just with double or triple the boredom.
Then, include/require free-diving skills to a much greater extent than has been my experience (and which seems to usually be the case). I'm in no doubt that if I hadn't already had the skills, a course like the YMCA/SEI curriculum would be my choice for giving divers some fundamental underwater experience, much of which transfers well to scuba: mask and snorkel clears and controlling buoyancy by lung volume are a few, not to mention mouth breathing through a mouthpiece. Personally, I'm really glad I learned to use a snorkel without a purge valve way back when; makes clearing a reg underwater without using the purge a non-event.