The need to start up possibly multiple engines to get full power is something I mentioned a while back as potentially an operating issue - a noticeable delay in getting the power desired. Over time, with training and experience, engineers would be able to adapt - much as they and truck drivers adapted to turbo engines that don't have instant response either.

While the gensets probably won't last as long as traditional locomotive engines, they are designed as the ultimate power module: if something that has to go to the shop for fixing, the shop can pull the entire genset module and plug in a working one, getting the locomotive back on the road while the problem is fixed. That's a theory and an advertising ploy; does it work in practice? Of course, it assumes that the shop has a place for at least a small inventory of gensets and somebody to maintain them pending use on the road.

Yes, there will be pressure to upgrade the emissions performace whenever a genset needs to be replaced, which will naturally be more often than for a traditional locomotive diesel. That's a Good Thing for those who have to breath the air nearby (the workers and the neighbors). It will of course end up costing more in the long run, but probably not a lot more than overhauls on standard diesels that update emissions (as EPA requires now for older engines and will probably bump up the stringency of over the years).

If there are still problems with the control systems, why? Gensets have been around for several (5+?) years now so the software should be patched. They should be at least at version 3 (old line: don't buy something from Microsoft unless it's at least Version 3 or, equivalently, Service Pack 2) by now.

"Chopper" controls are common if not standard in recent rail equipment. Nothing new there. Shouldn't have any different effect on gensets than on anything else.