The best episode is "Wej Duj" in terms of telling its individual story and has the adequate balance between "nostalgic references" and being an interesting show in its own right. This episode switch between the Lower Decks of the Federation, Klingon and Vulcan ship until the plots intersect at the end. Themes of the lower decks of each ship trying to impress their superior officer in different ways. There is element of the Pakled/Federation conflict that is relevant to the story.
"We'll Always Have Tom Paris" Is probably the funniest episode with the whole mystery of the bridge officer suddenly come back to life and most of the crew members aren't shock by this as it happens all the time and Rutherford tries to find out. However the bridge episode who suddenly is alive was the bajoran tactical officer Shax who you would have saw died in the last episode of Season 1 and hence if you haven't seen him die. Although the episode does tend to undermine the suspension of disbelief for the sake of humour and I didn't really like Boimler subplot. Tom Paris makes a cameo here.
However in terms of episode best signifying the improvement. I will say that "Where Pleasant Fountains Lie" and "Mugato, Gumato" shows Ensign Boimler no longer being the butt of the joke and have him being hero of the episode. Mugato, Gumato probably shows the improve dynamic better with Marriner being captured and Boimler and Rutherford having to used diplomacy with the Ferengi to save the day which is the role reversal of the first season where Boimler is the one who gets into trouble due to naivety and action hero Marriner saves the day. However "Where Pleasant Fountains Lie" is the more interesting episode with Boimler trying to outsmart the evil AI (by the way at the end of the episode you'll see an evil AI prison and there is a CBS logo AI in the mix. Is this a criticism of the CBS handling of Star Trek?)
"Kayshon, His Eyes Open" is probably not that good of the episode but it was the turning point and resuscitation of the whole series. In the sense that in the beginning it seems like it was one of the whole "Classic Star Trek is boring" message from the first season and than flipped the message at the end. The episode seems to be a meta-commentary of the clash between Star Trek as an action movie from the JJ Reboots onwards and classic Trek and is only interesting in that way but the actual plot isn't particularly interesting. I guess if you want to see Riker you could watch it.
The series still has problem
Marriner is still obnoxious even if it is tone down from the first season. She doesn't get into serious trouble for her behaviour.
there is suspension of disbelief issues although less exaggerated compared to the first season
There is also the issue of trying to fill in the episode with as much reference as possible and sacrificing the main narrative. It would have probably be better to focus on one reference and fleshing out backstory or what happen after TOS/TNG crew left rather than cram multiple reference in a single episode.
I wouldn't say it's a good show but it's now ok and watchable. However it does show some potential that perhaps the third season it could become a good show.