Former JET here. Sorry it didn't work out for some this year, but there are lots of other options, and there is always next year! If you can get it, it is a really great experience. Most of my current colleagues started with Interac, which is similar to an ALT on JET in some ways. They are certainly a popular and safe choice for coming to Japan.
When you first come to Japan, the country is totally the place to be. Fewer people who speak English (foreign or Japanese) and people are generally more interested in you because they don't get many foreigners out there. Plus the city you can experience well as a tourist, but to really experience the country you need to be a part of it. All around it is just the better choice (I think). I would avoid putting "urban" as a preference on your JET application because realistically speaking there is a very small chance you will get an urban placement, and thus they'll be looking for people willing to be out in the boonies.
Good luck to everyone!