Yes. MDS has proven to cause problems in virtually every engine on which it is implemented. There is a reason why Ford and Toyota have avoided it. Auto start/stop is just a "hack", not a real solution, to try to gain 1mpg. Internal combustion engines are not designed to shut off, restart, shut off, restart, etc. Hearing the starter spin up at every stop is annoying. The retail cost of an OEM alternator for a non-eTorque engine is $479. The retail cost of an eTorque generator is $1,235 plus $2,250 for the 48V battery. That's a difference of $3,006 for parts alone. Ram is clearly subsidizing the initial cost (i.e. getting a higher profit margin on the non-eTorque models) since the "upgrade" cost on the window sticker is only $200.
That said, my 4 day-old Big Horn has eTorque. I did not plan on getting it, but I could not find a truck I wanted (at the price I wanted) without it. The start/stop is the best on the market. Restarting the engine does not use the starter motor. But clearly no other manufacturer dedicates an additional $3k of parts to get auto start/stop. I would also be concerned about parts availability in 10 years as this is kind of an oddball system. However, I only plan to keep the truck 3 years so I'm not worried about it. In short, I like the way eTorque works, especially if it actually saves the advertising 2mpg in the city. But I'd be concerned about long-term reliability and cost if I planned to keep the truck past the 8yr/80k mile warranty on the eTorque system.
Regarding the MDS, I can definitely feel when it engages on the highway. There is a mild shudder if you put any pressure on the accelerator. This is when an aftermarket exhaust system would sound like shyte. You won't notice it if you're just coasting. So far it doesn't bother me. If it does, I'll just start engaging the gear limit (to 8) every time I start the car.