Very unfortunately, rather than to give us a fast catapult launch, the people in charge of TOS-R revised the entire original (and visible) intention and turned the shuttlecraft into some kind of chopper.
I'd say the TOS-R people put right what once went very, very
After all, the shuttle clearly is
a chopper, as soon as it gets out of the mothership. It definitely has no use for catapult launches when planetside, is capable of hovering and maneuvering at hover, and can land with pinpoint accuracy between the most challenging styrofoam rocks or papier-mache trees. Why would it stop being a chopper when it again enters the bowels of the Enterprise
? There never was any story logic to that, and the shuttlebay "turntable" and "catapult" design made no sense except as an extremely clumsy means of achieving motion with miniatures but without classic (and unconvincing-looking) stop-motion techniques.
The transporter somewhat mirrors the illogic. Machinery is required at one end, but not at the other - what's with that? But at least the transporter is magical. The shuttle is just a chopper that flies in space, intuitively familiar to the audience in all its characteristics.
Now, things could of course have gone differently. Had the shuttle been more like Jeffries' original aircraft-like designs, there would have been artistic merit to treating it like the auxiliary aeroplanes of 1930s-40s warships, with largish hangars, complex arrays of rails, switches, turntables, and a launching catapult. Hopefully, planetside action would have reflected the inability of the shuttle to land or take off vertically, too. But that's not what happened. Instead, we got a shuttle that by design has no use for turntables or catapults. Which is perhaps artistically less interesting, but makes for better scifi and cheaper production.
it will lead to a longer flight deck since the elevators at the end will add length
The thing we can do with a long shuttlebay is to divide the secondary hull functionally into lengthwise segments, rather than chop it up like a sausage. That is, the long shuttle facilities would take up the middle, while engineering would be atop (in TMP style, although various partitions make this "fact" difficult to see in TOS) and cargo systems below the shuttle section.
As to the differences between TOS and TOS-R, I put them in different continuities since the VFX is pretty different.
That's probably mandatory, alas. Each take has some pretty good ideas and some less interesting ones. I particularly like how TOS-R treated the ion pod...