It's a surprisingly mature thing to do to make a Doctor Who story about drugs (you may occasionally hear people claim otherwise; they can safely be ignored), and the fact that it's not terribly heavy-handed in its use is definitely in Nightmare of Eden's favor. It also helps that this story isn't just about drug smuggling: we've also got a problem with two ships that have accidentally merged with each other, a matter transmuter that might be unstable, and monsters from somewhere that appear to be roaming the larger of the two ships, the Empress. It's the collision that first interests the Doctor ("Of course we should interfere! Always do what you're best at, that's what I say"), and his unorthodox method for separating the ships is what drives the plot of these first two episodes. The drugs are still present, but they're not always the primary focus of things.
It certainly doesn't hurt that the Doctor seems very serious about what's going on, even when he's making light of the situation; much like in City of Death, here we get someone who's trying to put everyone at ease while he works out what's going on, and thus we get the impression that he really does care about things and isn't just clowning around for the hell of it. Lines like, "I value my life, and this machine makes me fear for it," while delivered rather off the cuff, still nevertheless convey a sense of gravity. And the depiction of the effects of the drug vraxoin, or "vrax" for short (presumably analogous to cocaine/coke), is surprisingly chilling; watching the navigator Secker laughing his head off while the Empress crashes into the Hecate is genuinely unsettling, as is the moment where someone spikes a drink with vraxoin that looks like it was intended for Romana but ends up with Captain Rigg instead.
Then there are the monsters of the piece, the Mandrels. While we don't really see them that much in these two episodes, I have to confess that I've never really minded their design. They do walk awkwardly, but other than that they seem quite effective to me. The hands are nicely clawed, and the growling sound they make is pretty scary. Rather less impressive is the bug that attacks Romana -- well, a "bug" was apparently the intention of the script, but all we get is a white light that could be just about anything, and it takes a number of viewings to work out what's actually meant to be happening.
But really, these two episodes move a long at a nice pace, keeping things interesting with additional discoveries, new problems, and lots of great dialogue (such as, "Work for? I don't work for anybody. I'm just having fun," the Doctor tells Rigg). It may have been a nightmare behind the scenes (more on that next time), but the result on screen is so far very good indeed.