To be honest, I've often felt that myself...based on what I've seen, the major differences are
-Aesthetic: This is a forgivable one, since most of the manga/anime people have heard of are professionally made, while most of the webtoons people have heard of are not. But yeah...usually the overall visual appeal of webtoons is a little lower. Whether the art is simple or intricate, it tends not to look quite as good as it could.
-Interesting Character Design: I have seen VERY few webtoon characters that actually drew me in at first glance (something that happens to me all the time when browsing anime/manga...). I think the vast majority of webtoon characters have fairly pedestrian designs, even when you take fantasy series into account, unfortunately.
I think this is because of the trend of patterning webtoon stories after live-action TV dramas, so artists tend to style their characters after real people, and dress them in things that real people wear...which tends to limit creativity.
-Humor: ...Most of the webtoons I've read just aren't very funny. =/ Like, either the humor is so basic that I can't really enjoy it, or it tries and fails so hard that the cringeworthy execution lives in my memory forever (true story...).
I could blame this on the 'pros vs. amateurs' thing again, but there are plenty of great comedy-focused webtoons out there...I guess more of the drama-focused webtoon writers just lack that talent.