What a strange quastion..... for same reasons why Chrome OS is niche, websites won't let you do everything, they are limited to what browser let you to do, Java is way faster then JavaScript and websites are not so reproductive as applications due to nature of HTTP. Using just websites would limit possibilities, i personally prefere using applications over browser
Also smartphone small screen does not excuse smartphone fr not using websites and HTML can be formulated for there size, in fact some applications are not really 100% but masked browsers displaying websites.