I chose the STC from Pponk. There's not much to the documentation, but I think less is more. No significant limitations. Not much in the way of instructions either, but it's very straightforward. You'd have to have done some homework to tell the two engines apart while hanging from the engine crane.
Very minor baffle trimming and fitting. The biggest stumbling blocks had to do with the oil filter housing. The throttle cable bracket attaches to the studs that hold the filter housing to the case on the old 520. On the new one, the housing is a bit different. One stud that I needed for the bracket is unused on the 550. I simply inserted a Continental stud bought from Aviall and a spacer that was as long as the old accessory case was thick. The second issue is that I've been unable to extract the oil filter from behind the seaplane mount without taking the starter off. A small PIA. I fly 100 hours per year, so it means pulling the starter twice a year. Big deal.
Skytech is working on a new starter drive and starter STC that will solve some potentially bigger problems, and this small one simultaneously in about a year.
As for the MT propeller, it is not on the STC from Pponk, but the Flight-Resource STC covers it. I like the MT. I chose it mostly because it weighs less and won't crush my engine vibration isolators as quickly. If I'd gone with a three blade Hartzell or McCauley, I think I WOULD HAVE found it necessary to install the SeaPlanes West engine mount with bigger isolators. Not required under the STC from Pponk, but I just hate saggy engines.
There might be a prop that gets me out of the water faster or cruises faster, or any other number of benefits, but I don't care. My airplane is quiet, and that's important to me. It's light, and I just don't like making a spectacle of myself, no other reasons.