3 wheeler (5 speeder) - Old school image - has more charm and if you get an upgraded example for reliability (Centa and Ohlins for example) then still perfect for touring (take a look at UK touring groups EU adventures) and also 2 friends of mine (each in their own 5 speeders) recently completed an 8000 km road trip - no issues. Prices seem to have stabilised.

Super 3 - modern image/styling - modern engine and electrical system - people who have had a 5 speeder before have said the Super 3 is nicer/easier to drive and after following Steve Morris at Grindelwald when the S3 was launched I can agree the S3 does handle well. Main Issues seem to be with the seating position (sit on rather than in the cabin), they are a bit of a handful in the damp ending in accidents....as well as the width of the front end on UK roads.
Possible future engine issues (although cheaper to repair than a 5 speeder...)
A concern of mine would be the plummeting prices, lack of support in near future (tyres?) and the fact that not many S3's have been sold - as wouldn't be surprised if MMC halted production/support in near future.
Complete lack of charm compared to a 5 speeder.

Personally go for a well sorted 5 speeder - not biased in anyway of course drive