I'm not keen about staying in downtown Jayapura, as there isn't that much to do there. Matos is located in Abepura, which is much more lively, being close to the Unviersity. The hotel is very clean and stylish and well managed for Papua. Few staff speak much, if any, English and it stretched my Bahasa to get the wifi turned on, but when it was it worked as well as you can expect in Papua. The TV channels are a little limited, as with most hotels in Jayapura. Food isn't great, but better than most places in Jayapura. Its also good value for Papua.
At night there are a number of restaurants nearby, mostly western fast food (Pizzahut is in the same building as the hotel and KFC in the shopping centre), but there is a charming Indonesian restaurant opposite the hotel. Also there are a number of warungs around the shopping centre close by, whilst none are brilliant, there is a good choice of food and they are cheap for Papua. You can also buy cans of very expensive beer ($5) in the supermarket at the shopping centre, which is hard to come by in Jayapura.
Well that's about it there is little else to do, so make the most of eating out and trips to the supermarket. Although if you do visit during times of political tensions, Abepura does tend to be the centre of any conflict, so you could find yourself in the middle of a standoff between locals and the military. Given that there is so little to do, you might even find this exciting.