Every command I've been in, the cardio alternatives (treadmill, bike, elliptical) have been a by-request thing. Only time I've seen a bunch of people did it on the treadmill was when the PRT overlapped with FCLP's and most of the pilots and FO's had to do the run on treadmills once we got to the Boat.
If you do a treadmill run exactly per the Navy rules, you have to punch in an incline (don't remember how much...1.5 or something). It's nice to be out of the weather, but that's about the only advantage. Never done the bike or elliptical, but mostly they're for guys with fucked-up knees, PFPS and such, not necessarily the old guys.
By the book, they don't have to offer the swim, but never been in a command that didn't.
This is all Fleet PRT's, of course. Initial-accession PRT's have their own rules. If you're a good runner, don't sweat the PRT much. I suck at running, absolutely hate it, have stumpy little fireplug legs and somehow manage to pass it with time to spare. So get through it with a good score, but not at the cost of injuring yourself. Keep yourself in good condition for OCS.