Mike,
It doesn't really bother me, and other than swapping nines, it has only happened a few times. Once was Opryland for the senior tournament they used to hold, and it resulted in back to back par 3 holes for the sake of crowd control one week a year.
In the few other cases, it seemed to work out fairly equally. While we do consider a balance of holes in routing, trying to mix short and long par 4, par 5 and par 3, etc., I can't say it really altered the course experience for most. Again, if there are 18 solid holes, that is all that matters in most cases.
Interesting on the par 3 thing. At the Quarry, proposed an 18th hole par 3, even contacted Ron Whitten to get a list of courses, including top100, that had them, but no dice.
Have a routing now, in already platted/built (partially) where a narrow corridor exists closest to the clubhouse, really only fitting a par 3 finish. Faces east, so 18 makes sense. We shall see.