But we all know that. The fun is in taking the stuff and trying to make it work, and discarding the rest with a grain of salt. To make it all come together, we have to be willing to make sacrifices. At least in the sense of reaching a consensus. However on your own, you can agree or disagree with anything in Trek.
Like for me, Not only is the a/am reactors in the nacelles, but they're very much integrated with the warp system and bussards. It's not like in TNG where you can apparently just open a hatch and slide the warp core in and out (quite sexy sounding though)! They're very big, very complicated, very dangerous engines.
Some may personally disagree with me on it. But I'm just basing my conclusions on my observations on the show- throwing in some stuff that makes sense to me, disregarding the stuff that seems silly, and trying not to make up too much fantasy for this sci-fi drama.
And all the while trying to avoid getting into unproductive arguments with fellow fans. I don't mind an argument as long as it's an exchange of ideas and points of views that don't piss on other people (unless the other person is being a douchebag- then I'm okay with it)...