It's actually pretty difficult for me to decide on which starter trio is my favorite. Quite a few of them have pretty strong contenders. After mulling it over for a while, I think it comes down to either Gen I or Gen IV.
Gen I: Bulbasaur, Charmander, and Squirtle greatly benefit from nostalgic affection for me. I'm not particularly interested in their middle evolutions, but Venusaur, Charizard, and Blastoise all have pretty great designs and Blastoise is one of my favorite starter Pokemon overall. Combine nostalgia, strong designs, and the attention they've been paid in recent years with Hidden Abilities and Mega Evolutions and they are very tempting choices for my favorites.
Gen IV: Not a big fan of Sinnoh, but I very much enjoy Turtwig, Chimchar, and Piplup. Torterra is an awesome looking Pokemon with a fun typing, penguins are my favorite animals so Piplup and its evolutions are great in my opinion, and Infernape looks fantastic and has the great Iron Fist Hidden Ability. Their typings and movesets are nice, and I gained a lot of affection for them after using them all in an Alpha Sapphire playthrough.
I think I have to give the vote to Bulbasaur, Charmander, and Squirtle/Gen I just because they've been given so much attention and love over the years
Honorable Mentions have to go to Gen II and Gen VII.
Gen II: The Johto games are some of my favorites in the franchise, and Chikorita, Cyndaquil, and Totodile and their evolutionary lines play no small part in why I enjoy them so much. Feraligatr has a great design and Hidden Ability, and to my recollection was the first Pokemon I ever leveled up fully to 100 back in Crystal. Also as much as I love a lot of the other Fire-type starter Pokemon and their dual-typing, there's something to be said of Typhlosion and its plain Fire typing. Meanwhile, despite also liking Meganium and its design, I don't like it nearly as much as other starters so it kinda drags Gen II down when comparing the trios like this.
Gen VII: I really, REALLY like the starter trio from Sun & Moon. Rowlet is hands-down my favorite first-form starter in the series, and all three Alolan starters have really great final evolution designs. Decidueye's archer design is great, I'm a lifelong fan of professional wrestling and love Incineroar's heel theme, and Primarina has a great look and interesting concepts behind its design. Despite all of this, I feel like both the Rowlet and Popplio lines take missteps that are kind of disappointing. Decidueye, while a great design on its own, feels like it's not related at all to Rowlet and Dartrix. Meanwhile, the difference from Popplio to Primarina is staggering and I don't feel that Brionne does a sufficient job of making the transition feel natural. Combine these issues with the terrible Speed stats of all three Alolan starters and it drags things down too much for the trio to be my favorite.
As for the others...
Gen III: While I really like the Blaziken evolutionary line, I'm not as interested in the Sceptile or Swampert evolutionary lines. They aren't bad, and I do like them, but they don't compare to the others.
Gen V: The Serperior evolutionary line is great and I like it even more now that it has had its Hidden Ability Contrary made available last year. I'm less interestd in the Emboar line but still like it, and the Samurott is just not very interesting to me.
Gen VI: The Chesnaught, Delphox, and Greninja evolutionary lines are all great in my opinion, but I don't feel as interested in them as I am the other trios.
TLDR; Gen I > Gen IV > Gen II > Gen VII > Gen VI > Gen III > Gen V