I think that the biggest problem with agriculture today is that it's utterly unsustainable. It is ran on fossil fuels and we need to mine minerals for the fertilizers. But still the most worrying issue is that the modern farming is consuming topsoil and we will run out of it in 60 years if we don't change our methods [1].

There are interesting things going on in regenerative agriculture scene where the main idea is to produce new topsoil and through that make farming sustainable. Here is a nice lecture by Richard Perkins - who is one of the most famous regenartive agriculture advocate - explaining the principles of it in a lecture he kept in a food hackaton. https://www.youtube.com/watch?v=3Knn7ZH4Tiw

(1) https://www.theguardian.com/us-news/2019/may/30/topsoil-farm...