This was an excellent time related episode, and a decent continuation of part one from the previous season. While I found that flaws and plot holes are present in other ST TNG episodes (a valid reason to dislike those), I disagree with other reviewers here who claim this is one of them - in fact, I believe this is one of the episodes having the least amount of flaws and plot holes, and that is something to appreciate, especially for a time travel related episode. I'll try to explain these supposed flaws and plot holes mentioned mainly by wesleyprang's and Qanqor's reviews (warning: long post):
All in all, a well made episode. The only minor flaw I see is having Guinan as a black woman in the high society circles of a 19th century US, only a couple of years after the American Civil War - it just isn't realistic. But then, there were similar worse flaws in other movies, and diversity was always preferred to realism (suspension of disbelief?). At least here Guinan's character is crucial for the episode, and Whoopi plays her expertly.
- "Guinan would want a job on the Enterprise, so Picard going on mission in order to meet Guinan is a flaw" (wesleyprang). Guinan repeatedly emphasized that she values trust much more than being in a place where everybody else wants to be (i.e. Enterprise), and her trust in Picard was the sole reason why she chose to be a bartender on that ship. She wouldn't have been able to trust Picard if they hadn't met in the past, hence Picard had to go on the mission.
- "Data pays Jack London lots of money, but has no money to pay Picard's rent" (wesleyprang). That is believable, since he had to buy a lot of other stuff for the device he was building, plus he had to buy the carriage he used to save the team from the police, so he may have ran out of money by the time he got to Picard's rented place. He was also probably searched by the police, so he had to stay low and avoid playing poker for money for a while.
- "The Devidians only prey on the sick and dying - people who are already in a hospital bed, so it's obvious that they take only what they need to survive; this makes them a threat to all Humanity - even though Humans are spread far and wide by the 24th Century". While from a natural point of view it is acceptable to prey on the sick and dying, in human society a crime is still a crime, even if you murder a sick person. Who knows, that person might eventually recover, if he or she wasn't preyed on. Plus, it's understandable to have a bias on not killing humans, if you are human yourself. Humans are indeed spread far and wide by the 24th century, but this might be exactly because the Devidians were ultimately stopped from preying on humans by the Enterprise team in their 19th century mission from this episode.
- "Except that there were plenty of Earthquakes in San Fran - one happened just a few months previously". We are not talking about now, but the time frame when the Enterprise team went on their mission, i.e. at the end of the 19th century. I don't know the specifics, but I believe that the writers were careful to be accurate in that regard for that specific time frame, considering they even had a line mentioning that there wasn't any major earthquake in S.F. for 30 years. That tells me they did research the issue a bit, so the line would make sense.
- "If Geordi was able to build a device having the needed sensitivity to allow for the phase change, why didn't they try that the first time, instead of risking Data?" (Qanqor). First, it was urgent, in order to stop the aliens feeding on humans, and secondly: using the device built into Data was accessible immediately, compared to Geordi building his own; it was safer and certain to work compared to an experimental attempt by Geordi; they didn't had to risk any actual human team lives; it allowed a slightly delayed vocal communication with the other team members (not sure Geordi would have been able to incorporate that feature into his own device). Also, if you watch those moments carefully, Geordi didn't say that he couldn't build such a device, he merely said that they didn't have one on the ship at the moment (except for Data's one, that is) - it's easy to overlook the possibility of building such a device, you naturally first think whether you have one at hand or not.
- "When the team is assembled to go after Data, its makeup makes no sense, and it gets worse, when Picard sends Worf back to the ship" (Qanqor). It does make sense. Crusher was useful to treat potential injuries to the affected humans, discover how the aliens drained them of energy, and maybe find a cure. Troi was useful in sensing pain from the humans the aliens preyed on, life or distress signs caused by a team member's potential capture in case they split the team to better find Data, and so on. Riker was useful too, since after Data and Worf, he's supposed to be the only male having the physical qualities to handle potential combat, and if the team split, he would command a team while Picard would command the other. If there was a slip up in assembling the original team for the mission, that had to be Worf, since his Klingon appearance would have caused huge problems in a 19th century Earth, but that is corrected when he's replaced by Picard. Worf is exactly the one that had to be absent from the team that investigated what the aliens were doing on the 19th century Earth and went after Data (his looks), and precisely the one that had to stay in command of the Enterprise near a hostile alien race planet (he's the security chief).
- "The entire, problematic appearance of the away team in 19th century San Francisco is completely skipped over." (Qanqor) Skipped over, yes, but not flawed. Unlike Data, they probably materialized in the cave from Earth (since they followed the aliens when going there), so their appearance wouldn't have been an issue, since no human was present in the cave. Their clothes could be bought afterwards, using the same trick Data used when he wanted to play poker: sell their partially gold-made subspace transmitters, since they had no use for them in a 19th century Earth and they would have easily have others made for them when they returned to the Enterprise. They weren't able to get rent money because that would have been well beyond the cost of a trasmitter, and they wouldn't have been able to count on dr. Crusher's "income" as a nurse, since she was just pretending to be hired, she was not actually working there (pay attention to how she doesn't turn her face to the doctor when he speaks to her in the episode, in order to avoid letting him know that she's not one of the actual nurses).
- "So wouldn't 12th century Europe at the time of the Black Plague make much more sense as a timeframe for the alien time travel than 19th century San Francisco?" (Qanqor) Definitely. However, it is never mentioned (and open to debate) whether this was the first time the aliens preyed on humans or not. Maybe they travelled to the 12th century Europe as well, and it just happened that their San Francisco time travel was the one where the Enterprise team could stop them, considering Data's head in that Earth cave, that triggered the mission. Not to mention that the tech of both the aliens and the Enterprise team would have been impossible to hide and tolerate in a 12th century Europe, where they would have been almost certainly accused of sorcery and executed.
- "Why on earth didn't Data and Guinan take Twain into their confidence?" (Qanqor) Several reasons come to mind: the Prime Directive, avoiding altering the current timeline, the difficult task of convincing a man with such strong beliefs as Twain that they were not "invaders" (remember, he wasn't convinced until he saw the 24th century realities and Troi made a case for many of the humanity's shortcomings being corrected in the future they lived in), and ... well, he was a writer, so his primary reaction would have been to let his readers (and the reporters) know about the whole thing. It's like convincing a TV channel not to run their most shocking news story - not going to happen.
- "Why is Twain portrayed as such a frothing Luddite?" (Qanqor) He is not portrayed as opposing new technology or ways of working - he's simply portrayed as someone who thinks that in this case, the technology is used to "invade" (or facilitate an invasion of) the Earth by some suspicious individuals. That is entirely logical and believable - after all, we have even today people that are very much adepts of new technologies, but who are worried or fear that too much of the new technology (or that technology falling into the wrong hands) would lead to bigger problems (artificial intelligence built into human-like robots or nuclear weapons are classic examples of this).
- "How it makes any sense at all that the only food these aliens can eat is human neuro-chemical energy." (Qanqor) Easy: it's the same as any of us preferring to eat cooked food over raw food, or chicken over pork, or diet food over fat-rich food, and so on. Food is not just a matter of necessity, but also a matter of preference. From our perspective, the neuro-chemical energy of a human, Vulcan, Klingon or that of a cow might look the same, but for such a race it might be that the human one is more..."tasty", maybe richer in their calories equivalent for this type of "food", or simply, more accessible than other types of neuro-chemical energy. Talking about accessibility, we know that the cave on Earth has a similar ideal configuration to amplify the phase shifting signals used to time travel as the cave on the Devidian planet, so they have a foothold on Earth. The phase change of 0.0040 used to time travel to 19th century Earth is very close to the 0.0047 change used to destroy the aliens, so it might be that the 19 century Earth was the closest food source for the aliens's time machine (after they probably exhausted the food available on their home planet).
All in all, a well made episode. The only minor flaw I see is having Guinan as a black woman in the high society circles of a 19th century US, only a couple of years after the American Civil War - it just isn't realistic. But then, there were similar worse flaws in other movies, and diversity was always preferred to realism (suspension of disbelief?). At least here Guinan's character is crucial for the episode, and Whoopi plays her expertly.