I agree with all the Gameplay Shortcomings. UFO is even more punishing when you make mistakes (that the Ufos encourage you to do). In SA you don't need to take risks, just play well. take this situation:
You are chasing the last Red Ufo to get an extra life, but it changed color at the last moment, and you got caught by a bullet that camouflaged with the background. Now, you lost 1Power, 1Life, Ufo lineup, and it was before Shou's boss battle. Did i mention you were playing as Reimu Homing (the character with likely the less amount of damage?).
That makes me want to throw this game out the window, more than SA (that it's fair but really hard) even if every other aspect is among the BEST of the series. I totally agree with Juunimeta here.
The Ufos are a good mechanic, but ZUN did a bad job at implementing them this time. Look at WBaWC, where it was so well done, the game is essentially the easiest if you know how to gather them.
Character wise, i think it has one of (if not) the best group of characters. ZUN fixed the issues with Touhou Lore being hidden away in text files not included with the game. Some things i like about the characters:
Byakuren has a point, she proved that if treated with respect, Youkai are great. I love the conflict it solves in Reimu, as she is in a moral corner to either go all out on Youkai Hunting to protect humans or let them run loose and threaten Gensokyo's balance. Byakuren can be the Youkai Protector and Reimu the Human Protector.
Nazrin (Stage 1 Boss!) is the catalyst to the story, as Shou asked her to employ her Radiesthesia to locate both the missing pieces of the floating vault and the Bishamonten Pagoda. The protagonists also unwillingly help out the cause by taking Nazrin's job to collect the "treasure". I really like that Nazrin used the Pagoda without permission, it gives her a lot of personality.
Kogasa is arguably the less memorable character, but she actually plays a role in the story. She is the golden example that "shot first, ask later" is a bad business model for the humans, as she (with Sekibanki) are among the least hostile Youkai, only needing to scare you to gather energy. Kogasa serves as the example that Byakuren is right with all the "Youkai forgiveness" (on other media, you can see Kogasa hang out with in Byakuren's temple).
I enjoy Nue just pranking everybody. She even makes cameos as the "Glowing Ball" (remember, she can change how you perceive her appearance).
Music wise, it has a great OST full of what now we can consider classics. My favorite tracks are Interdimentional Voyage of a Ghostly Passenger Ship (one of the few instances of the ZUNBass), Captain Murasa, Rural Makai City Esoteria and things like The Tiger-Patterned Bishamonten being among the most intimidating and epic tracks in all of Touhou.
Fire of Hokkai is pretty meh, but it really shows that Byakuren awakened with the heart beat as a drum
Extra things:
Byakuren's spell card, Great Magic "Devil's Recitation" and the fairies in Makai make pretty clear references to Shinki. Makai is depicted as a desolate place compared to Mystic Square.
It further solidifies my head-canon "Alice got the Grimoire out of control" theory. As you see a ruined Makai, with few traces that something once was there, probably the result of the destruction caused by the events in Mystic Square and the Extra Stage (where i think Alice in her egoism pushed the Grimoire too hard and unleashed some world breaking dangers). Reimu also remembers being in Makai, but she doesn't remember Alice or the other inhabitants of Makai, interesting.
At this point i should structure the theory better and make a post in here.
Another detail i enjoy is that the Bad endings are really BAD. You get stuck in Hokkai with no apparent way to get out, it really pushes you to complete the game.
There also exists a Touhou virus/malware someone made called Rensenware (joking with the japanese title of UFO), where Murasa uses her ghostly abilities to encrypt your drive, challenging you to score 0.2 BILLION in LUNATIC to decrypt the drive.
The funniest thing is that if the YouTube comments of the video are right, the author of the virus got himself and a lot of people infected and had to program a decryption tool to solve the incident.