I always love my rare opportunities to get above treeline and they rank among my favorite times in the mountains, especially on my few trips out West. But as others already pointed out, being alpine doesn't necessarily make it more challenging than a peak that isn't. And in the Southeast where I live, people like Peter Barr, Shane Ashby, and myself would never get above treeline. But I can assure you that we've worked harder and suffered more to bushwhack up many of these rhododendron and briar infested 2,000' - 6,000' peaks than we have on any alpine peak with a trail. One can hardly say they don't count as peaks just because they have trees on top.
It's all good, and they all have their own rewards and challenges. Just for the sake of discussion, I fully understand and agree with the reasoning of a 300' (or whatever) prominence cutoff for being a ranked peak but that alone has absolutely nothing whatsoever to do with how difficult and how much of a challenge it was, or how rewarding it was. One perhaps extreme example would be in the Indian Peaks Wilderness of Colorado. I haven't been there but I've seen pictures and read up on the area. It would probably be untrue to say that someone who climbed Apache Peak (El-13,441', Pr- 1,101') http://listsofjohn.com/PeakStats/Climbers.php?Id=362
had a more challenging and more rewarding and worthwhile experience than someone who climbed nearby Lone Eagle Peak (El- 11,900', Pr- 40') http://listsofjohn.com/PeakStats/Climbers.php?Id=1799
, which when viewed from the North must be one of the most amazing sights in Colorado. And it could be considerably more challenging to spend an entire day of continuous steep ups and downs on the forested sub-4,000' peaks of the Mahoosucs or the Devils Path in the Catskills than on the generally less steeply graded ridgeline traverse of the alpine Presidentials, especially if you drove up to Mount Washington first, as opposed to one of the hideously steep trails from the valley. There are countless examples closer to my home where a lower mountain is both more challenging and also more rewarding for views than a nearby higher peak that you can driver higher on and closer to that has no views. Just as the exact opposite is equally true.
My two cents for what it's worth,