Great idea. - The frontpage should directly show the list of papers, like with HN. You shouldn't have to click on "trending" first. (When you are logged in, you see a list of featured papers on the homepage, which isn't as engaging as the "trending" page. Again, compare HN: Same homepage whether you're logged in or not.) - Ranking shouldn't be based on comment activity, which ranks controversial papers, rather papers…
I don't think this is an inherently better approach, but maybe there should be an option for different ranking mechanisms. You could also rank by things like cite-frequency, cite-recency, "cite pagerank", etc.