This is an episode that will likely split the fans right down the middle, and could easily alienate those tired of the seemingly endless Clark/Lana romance. Despite my own leanings in that direction, I actually liked what this episode was trying to accomplish. I'm not sure that the script was able to handle all that exposition particularly well, but many mysteries are resolved and the implications are promising.
The character of Lana has always been frustrating, because the men in her life have always managed to treat her less as a person and more as a possession. Lana has occasionally struggled against that role, but as she notes to Mercy in this episode, fighting Lex on his own terms is still, in a sense, allowing him to control her life.
Similarly, running to or expecting Clark to save her is little better. The catch is finding a way to stand on her own two feet, and Lana has determined that Project: Prometheus is the means to that end. It's an evolution of what Lana originally started with the Isis Foundation, but without the singular goal of taking down Lex. (According to Lana, preventing Lex from getting Prometheus is just a convenient side effect.)
Lana's ability to withstand crippling pain and fighting prowess seems a bit much for what is, in the end, a matter of months in continuity. Even so, that could be an actual plot point. By the end of the episode, when Lana has been altered and powered by Prometheus, she seems to think she's invulnerable. That could be a major mistake.
From Lana's perspective, this allows her to be with Clark without wondering if she's holding him back from his true purpose. Even Clark doesn't consider himself to be invulnerable, and since Prometheus is based on Kryptonian technology, there are some obvious potential weaknesses. This seems like a classic case of overconfidence. With Doomsday still out there and Mercy's intentions still open to interpretation, there are plenty of scenarios that could lead to Lana's untimely demise. Or, it's equally possible that the experimental nature of Prometheus could lead to some serious health issues, thus forcing her to leave Clark behind to find a cure for her condition.
Whatever the case, it seems unlikely that Clark and Lana will be together much longer; this entire exercise is meant to bring Lana's character to a more fulfilling resolution within the series and to provide a look into Lex's current status quo. All of that serves to advance Mercy's character arc as well.
Kudos must also go to Allison Mack for her directorial debut. This was obviously a technically challenging episode to direct, yet she managed to pull it off very well. In fact, it rivaled some of the direction we've seen by the usual suspects. Let's hope she gets the opportunity for a follow-up in the future!