I thought the nacelles looked a little thin at first too. But the more I look at it, the more I like how the elements evolved from the original series shuttle into this one- and one of those elements are the nacelles. I kind of like that this is a future version with SMALLER nacelles. Kinda makes sense that some things actually got smaller as the technology improved over 100 years.
I love this ship- the Runabout from DS9 was clunky. It had so many lumps and crap on it, you'd think the design team was on future space crack.
AS for the backward facing bussards on the bottom, like the other transport shuttle they had it on, I just take it with a grain of salt that it's a design element that just LOOKS like them... There's only so much we can rationally explain away.