I've used both, so I can tell you my experiences.
Sustanon needs to be injected every 2-4 weeks, depending on what your t levels are. Normally it's 2 weeks, but I had to try 4 as my levels were sky high. The upside is that you, or a family member, can inject it, so no need to go to a doctor or nurse. The downside is that you need to inject often. Due to it's short release, your bloodlevels spike a lot. This gave me huge issues with cystic acne and I had to try Nebido.
Nebido is slow releasing and usually injected every 3 months. The upside is thus that you don't need to get injected often, and your bloodlevels are a lot more stable. Nebido did not give me acne. The downside is that you need to have it injected by a nurse because it is a lot of fluid, and the fluid is quite thick, so difficult to inject. It also needs to be injected into your bum, so yeah...Quite impossible to do it yourself. But seeing a nurse about 4 times a year could be worse.
My personal preference is Nebido as you can just forget about it for months after your injection. When I was still living in Holland, Nebido was expensive, though. It wasn't covered by my insurance, so I had to pay 90 euros for one shot. Sustanon was free. I live in the UK now and was astonished to discover that Nebido is just as cheap as Sustanon. I assume this is the case for everybody in the UK.