It is recommended that a stroke index allocation be applied over 18-holes, split into six triads with each hole ranked on its playing difficulty relative to par. The difficulty of each hole can be determined objectively using hole-by-hole data provided from the Course Rating procedure as follows:
From the USGA.
That recommendation is less than a month old at this point, and many (possibly most) courses are sticking with their old stroke index assignments. They have no incentive to change it if it's working just fine.
In the old system that's still the current system used by the vast majority of courses, par fives were often 1-4, with par threes 15-18 (or very close in both cases) because… they're the holes where the higher handicap player was most likely to need a stroke against the lower handicap player.
Par fives are almost never "the difficult holes" for good players. Those are the par threes. And the situation typically reverses for the higher handicappers: they often get higher scores (more chances to hit a poor shot) on par fives relative to par than on par threes, where they often just made a 3 or a 4. The USGA has a ton of data on this, because courses used to submit about 500 scorecards, scores would be entered, and the computer would tell you which holes to give what stroke index based on what I just wrote: the holes where the higher handicapper needed a stroke. (Now they can get that data from people entering Hole-by-Hole scores.)
Edit: Why change it? Because it's a pain in the butt to submit 400 or 500 cards, enter them all in, etc. The new system is significantly easier because it just uses existing course rating data. And let's say it shows that a par five is going to be 4.9 for a scratch golfer and 6.2 for a bogey golfer… and a par three is 3.1 and 3.8. Relative to par, the par five will still show as a lower stroke index (+1.1 vs. +0.9), but still, for the scratch golfer, the par five is not "more difficult." And in the new system, courses might find that handicap holes 1, 2, and 3 are in the first five holes, and they'll shift stuff around even then, to arrange them in "triads" and split them across the front and the back, primarily, so that further removes them away from even this version of "difficulty."