This series starts where the previous season/series ended. There is an intriguing network of interconnected events woven together like a spider web that culminate in the final episode. What you are left feeling from it maybe a bit convoluted and up for debate.
***Spoiler***
It is hard to say what the ending sequence suggests. Could Jun be the father? Just a student/apprentice, or some heir apparent? Either way it is at least strongly implied that Jun carries the same skills, attitudes, and personality as the father or at least something similar. He was trained how to make dolls from scratch which is something not seen in season 3. This makes Jun feel like an even stronger candidate to either be father's reincarnation or to be his successor. Though it is unsaid, it could even be possible for the viewer to believe the doll shop will reopen eventually with Jun making the dolls and Laplas once again taking human form to serve as the shop keeper.
Perhaps the introduction of the apprentice twists things up a bit in a direction never envisioned in the manga and the creators were hard pressed to resolve the matter. Maybe that is why parts of this story get a bit muddled. Also, I felt strongly the fact that #7 fell in Jun's dream might have some future connection and consequence. Surely they could have done more with that, but sadly instead they seemed to have chosen to ignore it altogether.
***Spoiler End***
Laplase is a huge mystery in every season, and his role nor his origin or interest as it relates to what his motivation is, is ever revealed, well at least not fully. He therefore remains a mystery. I must confess some characters come out as stronger and in a sense improved in season 3 than in the other two such as, doll #7. Seven seems a bit too dull, dead pan, and dispassionate at least until the very end of the series. In season 3, however her nature is given much more screen time for the audience to peruse and understand. In a sense, in fact, she becomes the focus albeit a bit oddly to the neglect of both versions of Jun, Seito, Tomoe, #1, and Shinku, though in fact Shinku suffers the least. That is part of the problem in a sense though cause it feels like it focuses too much on her. Season 2 did not have that issue and for the most part, shared time relatively equally with all major figures save the obsessed doll lover, Tomoe, and the girl on her death bed. Though the time with #7's master was well spent good quality time, it was far short of the others and her personality and character demonstrate severe limitations because she is too focused on a narrow view of things. Here too, Season 3 did more justice to that character. Shingatou (#7 or whatever the spelling of her name is) is a central figure of this and the ouverture.
***Minor spoiler***Between the two we get a much deeper understanding of what she is and who. It is a bit puzzling however about the amnesia which is also never fully explained or how she or her rose mystica got free of Jun's dream. ***Minor spoiler end*** ( I say minor because this information is revealed within the first 4 or 5 episodes or sooner.)
We do get introduced to the last 2 dolls. However, #2's role is a bit murky. She is also a tad more critical to the story in season 3 but less time is spent overall on the development and complexities of her character, so she is sort of a middle ground character as to how season 2 and season 3 dealt with her. The only other little flaw is that Jun seems to grow a bit more in season 2 but it still seems to take a long time. Season 1 probably dragged some of these changes on a bit too long and may have given a little handicap to season 2. They are overall good solid characters with ironically and a nod to humor, more life than the characters of a great many other anime and other media.
***Minor spoiler*** (Though it is not revealed how they actually come to life or what magic or technology is really behind it or even why only 7 were made and yet more dolls that could come to life seemed to be implied were being made. (See the one that the doll maker makes with Jun.)) The odd way they direct that it can save real human lives too is a bit odd, out of place, and confounding. ***Minor spoiler end***
So a few holes could certainly have been plugged and solidified the story much more. It may have been intended to have a season 3 that picked up where season 2 ended that never came around. It is a pretty good follow up to season 1 however, it still left a few things bouncing around in the heads of viewers. Wether that was intended to be addressed later in another season is no matter, since whatever they may or may not have intended did not happen. An ova or a movie or something could have put viewers to ease had they given the thought of a what if they could not make a season 3 just so viewers could get their deserved full closure. That might be a nice unwritten rule to have, make a back up plan so that stories can have some sort of ending rather than none where applicable. Even without full closure, most of the things were more or less resolved and at least some of those not resolved were given the impression they would be, though the viewer may or may not ever know what those were.
It is a fun show overall and oddly enough, it was better than the season 3 that supposedly followed the manga. This one has a bit more of a tragic element than any other season. At least that part has some ending conclusions you can rest upon after getting past the trials of emotional tragedies. It is worth the time I think as it has its own rewards to watch the series. It may even be worth watching season 3 for comparison if nothing else.