I think BMW is starting to make bikes with catalytic convertors and I think honda has sold a few models with them, and fuel injection has been available for a while, which makes a difference, 2 strokes are bad but alot of scooters are available in 4 stroke and also with fuel injection, the data the environmentalists are using is probably old, eco groups have a broad range of credibility and many spread misinformation to further their own agenda, imagine that.
many enviromnmentalists are reaching for pie in the sky solutions (electric cars) and when something already exists (motorcycles/bicycles) they will knock them with false data, the best way to compare is the total energy consumed over the lifespan of a product from beginning to end, since fossil fuel are used in every step we need to keep track of the product from nuts and bolts to the finished vehicle past it's usefull service life and how readily the materials are recycled, aside from heavy use by a racer a good bicycle trumps all other forms of transportation in that analysis and I would bet a motorcycle or scooter would come in second, scooters tend to be more cheaply made so a shorter usefull life may affect them.
also no one ever takes into acount the pollution cause by fixing road surfaces because of damage cause by cars and trucks, if everyone road a motorcycle our roads would last forever with minimal repairs, a perfect example would be a racetrack that has both a MC and auto track like pocono in PA the road course for the cars is all torn up while the special MC track is still very smooth,