Because of the mentality that people have, you included by your post, they are not regarded as rare as others. Since you do not see them as valuable, you do not want to pay more for them. It's a Catch-22. You don't think they're rare, so you don't want to give them proper value. And since they don't have proper value, you can't regard them as rare. It doesn't mean they're not.
As much research that I've done over the years, I can say that yes, they are definitely up there. Since I stand no chance of turning the NA tide, no one will regard them differently so as they are, they stay.
Also, your statement may be true if it wasn't for the precedent set by early collectors and Funco prices. Bubble Bobble 2 had one of the highest prices at the turn of the century at Funco. Since many, many early NES collectors, myself included, had little to go on with value, we turned to what resources we had, those being the Funco list and sadly, these abortions of the Etler list:
http://deathspork.flyingomelette.com...treat/rare.txt
http://www.nintendoplayer.com/collec...pdatedrare.txt
Look how Bubble Bobble 2 on both lists is one of the highest priced titles. Titles like Little Samson and Flintstones 2 miraculously went from <$10 to >$40.
Another thing to remember is while a good many NES collectors have found their way to DP and NA over the years, there is still quite a few who do not rely on either for assistance. All they do is google "nes rarity list" and they are taken right to the second link above. This is the way it's been for 10 years! Over many years, prices were influenced by, to be blunt, poorly informed collectors solely using eBay.