The Napier Turbo chargers were one of the main problems for the Valentas in terms of emissions, as they have such a long spool up, during which time the engine isn't getting enough air. This is even more true as old fuel control systems would just begin dumping more fuel into the cylinders with no regard for if the conditions were right for it to burn. That's why old engines clag on applying power, Valentas in particular. Driver applies power, fuel system chucks more diesel into the cylinders which are too cold and can't pull enough air in to burn it, and the result is a fair amount of unburnt hydrocarbons, partially burned fuel, Carbon Monoxide and foaming enthusiasts. As I said before though, CO2 emmisions arn't effected. The most efficient engine will just make sure all the carbon in the fuel gets turned into CO2. Modern engines like the MTU (and the VP185) have multiple, smaller turbos which have much less lag. Some use variable vanes too for even more efficiency (not sure if any railway types do). That is combined with modern fuel injection systems which make sure the right amount of fuel is injected for almost complete combustion, and you've got a slightly more efficient (since more fuel get's burned and converted into useful energy, not just blasted out of the exhaust and turned into enthusiast porn), and much "greener" (from the point of view of particulates and HC emmisions) engine.
Just another thing regarding the MTUs and Electrification. I'm not familiar with the specifics of the railway emmision rules (road vehicles are another matter), but it was mentioned on the GC MTU discussion that the MTUs from next year would not be able to attain the standards for new engines, hence why GC are rushing to get all their powercars done. This oviously would rule out the MTU for a future Diesel HST replacement. Developing a brand new engine would push up the cost dramatically. There is also the question of the QSK19s which are the ovious choice for an underfloor engine high speed DMU, being fitted to 22X, 180 and 185s. The smaller engines on most DMUs are far more economic to develop to keep up with changing emmisions standards, not only being far more common on local and regional DMUs, but also being similar or identical to those used in the road industry. The same applies to the big, low speed lumps used in freight locos, as well as power generation and shipping. Engine choice could play a very big role in the choice of HST replacement. Electrification of the high speed sections would deal with that problem. Sourcing a suitable engine for hauling trains off the wires (that didn't need dragging dead under the wires) where speeds would be lower (100mph max) would be far easier.