I am obsessed. This app is amazing and is especially helpful if you are looking for flights on specific dates. If you are Type-A like me, you love to plan and plan early. I know where I want to go during a specific time and I make it happen. Hopper helps you determine if the specific flight that you want is at its cheapest price.
For example, I know that I want to go to Palm Springs from April 27-30, so I punched in those dates into Hopper and I sat and waited. Hopper tells me right away if its the best time to buy or it will tell me to wait. It turns out that it told me to wait and a couple weeks after putting that query, I got a notification from Hopper that I should buy now. Now I have a direct flight to Palm Springs on JetBlue for $230 round-trip. It's pretty amazing. Especially, since my friends just paid $400 for almost the same flight.
In terms of limitations, if you are looking for specific times on a specific date (for example, if you know you want to leave in the morning), then this app won't do it for you. It will give you the cheapest flights without consideration for time. Also, if your trip is a month or so beforehand, then it is likely going to just tell you to buy.
Pros: Saves you money (for real!) and its nice to get those alerts for an awesome deal. Also, if you have some flexibility, you can get an even cheaper flight.
Cons: Specific flight times are difficult. Also, if you don't plan far ahead enough, it will likely just tell you to buy now. Finally, Southwest flights are not available on the app.