After SD2K's accident, we don't really know what got changed. The trains and track cosmetically looked the same, but for all we know could have been completely new trains under the fiberglass shells, and most likely had all new inspection criteria and operating procedures added on top of Morgan's original requirements.
Of course as mentioned, many parks got caught out for not performing the required maintenance during the post Fujin-RaijinII fallout.
For me, I like the new trains. I think they look great, and bring new life to a pretty awesome ride. Fuji-Q has replaced the trains (or at least the leading fiberglass shell and paintjob) on Fujiyama a bunch of times.
I also wonder who approached who to do this. Since they spent @ $25-milloin on the original ride, I wouldn't be surprised if they threw money at Walter & Claude until they agreed to do it. At the same time, B&M has been doing some slightly more 'adventurous' things (at least for them), so maybe this was their idea. Either way, it's awesome, and I hope to see some other rides get refreshed in this manner.
As far as the leg bars, most Japanese people I observed on rides tend to behave quite well, keeping all arms and legs inside the ride vehicle, so to speak. However, the new seats appear to be quite a bit higher than the old Morgan benches, so there could be something related to the clearance envelope with the new trains, and this is certainly an easier fix than replacing a support or catwalk on one of the world's biggest rides.