This review has very minor spoilers, which I have carefully and somewhat ambiguously worded to spoil the least amount possible. This review is from the perspective of a fan of the visual novel that rewatched the anime a year later.

Positives:
-Kurugaya: Kurugaya's route isn't a very good adaptation, but it makes drastic changes that, in my opinion, improve upon some scenes from the visual novel. While yes, it is missing the great romance and the chemistry between Riki and Kurugaya it makes drastic changes to fit the anime story telling, which in my opinion works better as a whole for the story despite its very fast pacing compared to the VN.
-Beautiful new original opening for this season with an original song.
-Refrains story is all covered and unchanged.
-It uses (mostly) the same soundtrack.
-Komari and Rin's friendship building from season 1 into Refrain is a very nice touch that fans (including myself) appreciate.
-As said for season 1, Riki's voice actor/actress change to Yui Horie is an improvement; her voice suits the role better.
--There's a minor improvement in animation in general from the last season.

Negatives:
-Massive lack of CGs referenced. I can only think of 3 of the many many CGs in the VN that actually get used as references. They would have drastically fixed a lot of the poor production.
-Komari and Rin: My favourite scene in Little Busters as a whole is entirely and utterly obliterated by horrendously brushing over the scene. The most ridiculous part is that they spend 15 minutes building up to it really well, adapting the VN almost perfectly, but don't flesh out my favourite scene in the series. Making it feel soulless. Also, the direction/story boarding is awful, with really weird camera angles. Are we really so apposed to just using the CGs in the game? It looks so tacky.
-Rin 2 not adapted fully: Rin and Riki's scene in Kyousuke/Rin's grandparents house is supposed to go over the course of 3 days, not one evening. Ruining Riki and Rin's character building for the conclusion (making it less impactful).
-Kyousuke's backstory reveal: It looks like it's made in Windows Movie Maker because of the weird editing used for added content for flashbacks. It looks more like a fancam than a serious scene. 
The climax scene of the series: While it is a good adaptation of the story and follows the VN the production quality looks bad, not awful. But it's remarkable how the PNGs in the VN tell the story better than the full animated production. A lot of the camera work is poorly directed, as if it's some sort of fanfilm or a student project. It clearly has some passion behind it but it looks so messy. Mostly, the way characters fade on screen looks very tacky and unprofessional. It would have worked a lot better to moving the camera or changing the focus (like Angel Beats for example).
-Rin and Riki rescue scene: Changed soundtrack ruining the tone of the scene. (I won't complain about not seeing the bad end in the VN as that's difficult to replicate in anime format.)
-This is carried over from the first season, but the different art style lacks the charm of the VN.

Overall, the anime for Refrain, while I do think it is the best adapted content of the visual novel I think for an anime adaptation, it's mediocre at best; the production quality is a worse way to experience the story than just reading the visual novel, where it's a much better experience of essentially the same thing. Even though it's essentially PNGs over actual moving animated frames, VN has better visuals overall, over the anime adaptation.
While this is a mostly negative review, this adaptation is definitely serviceable compared to a lot of worse adaptations for things out there, but I still think it's a mess that could have easily been a lot better with a little more thought put into it. Before reading the visual novel, I originally had the anime at a 9 and even during reading it, I thought it was a good adaptation. The reason why is because story wise it was ,it's visually I'd forgotten how it'd looked.

My Anime vs VN Ratings:
Kurugaya route - anime: 8.5/10 VN: 7.5/10
Refrain - anime: 6/10 VN: 9.5/10