1 They were both made by the exact same person (Toby Fox)
No, Toby worked on music for homestuck and was friends with the creator, but the creator of Homestuck is Andrew Hussie.
Toby didn't make Homestuck, Andrew Hussie did. Toby just helped out.
2 They were both extremely overhyped by their fandoms yet criminally overlooked by basically everyone else
3 They both have this one obnoxiously overrated character that got popular mainly because of Megalovania (Vriska for Homestuck, Sans for Undertale)
I think Toby left a mark for Megalovania on all fandoms.
4 They are both incredibly weak visually, yet unbelievably strong when it comes to writing
Are you SERIOUS? The artwork for Undertale may not be the best, but it has its charm definitely. Homestuck got more and more artistic by time.
Actually homestuck's art got REALLY good.
5 They both have a main protagonist who is incredibly generic and lame compared to the other characters
Homestuck doesn't really have a protag, people just consider John to be the protag because he's the first one introduced. Still, it's true that he's one of the least interesting major characters, although he's still a good character because Homestuck doesn't REALLY have any characters that can be considered "bad". I'll give Undertale a pass on the uninteresting main character front because that's really the best a game can strive for if it wants you to be immerged in the world of the game.
6 They were both incredibly cheaply made, especially considering how exceptionally brilliant and well-done they turned out
7 They both have titles that are painstakingly obvious pop-culture references (HomeStuck = EarthBound, UnderTale = CaveStory)
8 They both have one of if not the greatest soundtracks to ever grace their respective mediums
9 They both feature Megalovania as a more-or-less-final boss theme
10 They both make fun of various tropes present throughout social networking and role-playing games
The Contenders
11 They are both more-than-frequently referred to as cancer on the Internet
12 They're both exceptionally weird in their own rights
13 They both feature that one adorably dorky girl that wears glasses (Jade in Homestuck, Alphys in Undertale)
14 They both feature ludicrous amounts of dialogue between characters
15 They're both immensely story-driven
16 They're both positively overflowing with fangirls
17 They both take place in astonishingly unique and creative environments
18 They both have extremely implausible amounts of pornography in their fandoms
19 They both have a major overabundance of pedophiles in their fandoms
20 They're both something that you pretty much either love or hate
21 They both feature gratuitously sexualized anthropomorphic fish women (Feferi in Homestuck, Undyne in Undertale)
22 They both have profoundly annoying yet strangely endearing styles of humor
23 They both feature at least one buck-toothed character
24 They both feature eldritch abominations (Cthulhu Monsters in Homestuck, Omega Flowey and the Amalgamates in Undertale)
25 They both star a vertically-challenged young child as the main protagonist