Ah, yes. Cave Story and Undertale. Two one-man indie successes (Technically, Undertale had minor help from others, but whatever) that have/probably will have a semi-cult following and also have excellent game design. Not to mention both are inspired by Nintendo-titles. (Metroid and Earthbound respectively) I hear a lot of people comparing the darkness of the story and the music of both games, so I think I'll talk about those specifically.
The music in both is, no doubt, amazing and very catchy, but comparitively, Cave Story's is much catchier and, in my opinon, better. Don't get me wrong, I catch myself singing along to songs like "Ghost Fight", "Bonetrousle" and "Hopes and Dreams" all the time, but I can pick out a vast majority of the CS soundtrack (like, 33 of the original 49) that I like. For Undertale, I can pick out 20-30 good songs out of its 106 song soundtrack. Plus, until I find a song that is on par or better than "White", CS will have a better soundtrack. Also, I find Toby's constant reliance on motifs a bit annoying. Not that they're bad motifs or anything, I personally love them. But at first, I found it cool, especially while in the game, where you naturally listen to the tracks, but listening to them out of context sorta makes me feel like, "Okay, I heard this melody 3 songs back, can we move on Toby?" Its also pretty dissapointing to hear this soundtrack after hearing his full album and various works in Homestuck. I'm probably ingnoring his more original works in the soundtrack, like "Enemy Approaching" and "Heartache", but I still think they aren't as good as CS, despite being more emotion-inspiring that CS at times. Speaking of which, the CS soundtrack is gold and to make things better, Danny Baranowsky, composer for Nicalis, said in a interview that Pixel couldn't even read sheet music. That's absolutely amazing for someone who created 49 original, (barring Jenka 1, I guesss) songs for his game, using a program he created and programmed and using samples he programmed himself. I find that impressive and inspiring. Despite thr fact that the CS soundtrack is less advanced and varied than Undertale (that is to say, Undertale has a lot of instruments at its disposal, from 8-bit to real instruments, and the soundfonts of Megaman X to Mario Paint. CS has variation as well. But more in melody style and notation. Many of my favorite songs ("Cave Story"and "Safety", to name a few) are done in 3/4 or 6/4 time and Labyrinth Fight has an old-school rock 'n' roll feel to it, whereas White has the harmony and beat of an R & B song. The Way Back Home has a relaxing bossa nova feel to it and Jenka is a straight up folk song. Maybe it's because of CS's wonderful developmental backstory or nostalgia blinding me, but I prefer CS's OST over Undertale's.
The dark story is something else entirely, though. Both do the "Cute, lovable characters; dark story" thing, but Undertale does it better. With CS you sort of have to think about the things happening in the game to understand why it's dark. The above comments do it better justice. From the Mimigas reverting to their original form before dying, to Hero's End. Ballos' tortured past and pretty much everything surrounding Curly. But CS does its darkness subtly, making the bright, bouncy visuals and music seem like a facade. That's pretty genius if you ask me. But Undertale, Undertale has better characters and world-building. But is an RPG, that's kind of expected for an RPG, especially a JRPG. It has better, more varied and developed characters that play off of each other. The world is so very interesting and cool and every second I spend in it is absolutely amazing. I will say that both games have intersting NPC'S and hidden goodies for those who look for them. However Undertale still beats CS becasue of it's Earthbound-inspired, and ever so witty dialogue. I love UT for it's story and characters, CS for the music and gameplay, and both for their charm and new things they each bring to their respective genres.
On that note I don't like Homestuck. It started out alright, but it became boring and full of long and mostly redundant Pesterchum logs. Problem Sleuth was way better. Cue shitstorm.
There's no shitstorm here, man. Just me. Quoting and commenting on your post. So it's more of a mokey flinging their feces as opposed to a cylindrical wind funnel of defication.
What I find weird about your comment is that the general consensus (at least on reddit, youtube and tumblr) is that the first 3 acts are boring and the 4th act and ownward is where the story picks up and gets interesting. Your comment is quite the contrary to the majority and I find that interesting. Very interesting.
I read Problem Sleuth and many of Hussie's other adventures after Homestuck. And because of how accessible Homestuck makes all of his previous works seem, and how you can see how all of their elements in HS, I found them much more enjoyable. But that's just my opinion, you're free to yours and I respect that.
Can I ask where you stopped off at? Becasue the intermission part between act 4 and 5 are pretty Problem Sleuth-esque, and there are various references to his previous sprinkled throughout.