I'm gonna base these less on ability in battle and more on aesthetics (as I do a lot of Pokemon):
Gen 1: The Charmander Line. I always thought that Charizard was kinda overly-popular. I think that Mega Charizard X looks pretty cool, and the other mega is okay, but Charizard itself is nothing I get hyped over. I especially dislike Charmeleon, idk if it's because of the red color or the weird spike thing on the back of this head (which I know is a logical design choice because Charizard has 2 spikes, but it still looks really weird. Like a Parasaurolphus or something.)
Gen 2: This one is a really difficult choice, because I like all 3 of the starters and their evolutions a lot. I would prob say the Chikorita line. Even though I love the overall aesthetic of Meganium, I'm not a fan of either of the two before it.
Gen 3: My least favorite for this generation has always been the Torchic line. It used to be because I always had something against Fire types when I was younger, but now I just prefer, say, Sceptile and Swampert over Blaziken by a lot. Though if I were to judge the fully-evolved starters based on their mega evos, I would say Swampert is the worst (it's so ugly!!!!).
Gen 4: The Chimchar line. I think Infernape is okay, but I'm not a fan of the designs of the two before it at all. Especially Chimchar itself, it looks really derpy to me for some reason. Though I have to say, I like Infernape more than Empoleon.
Gen 5: The Tepig line. I think, aesthetically, Serperior and Samurott look a lot cooler than Emboar. I actually think that Tepig is really cute, but I don't like the design of the next two, even though they make sense based on their (unnecessary) fighting-type.
Gen 6: The Froakie line. This is a similar case to Charizard; I think Greninja is too overly-popular. Like there's not really anything interesting about it, and seeing it constantly makes me grow tired of it really quickly.
Gen 7: This is probably the toughest one, since I absolutely love all 3 starters in this generation. if I absolutely had to choose one... I couldn't possibly do it. I literally just tried to come up with one that I didn't like and I couldn't. I guess
maybe Incineroar because of his ridiculously big, rounded, and weird paws, but that doesn't even bother me.
So there ya have it. My least favorite starter lines by gen