I like that progression through Kanto isn't a straight line. Sure, Pallet to Viridian to Pewter to Cerulean was, but that's the start of the game (and you could wander off west of Viridian for a bit). When you get to Cerulean, where do you go? There are four routes branching away from it, so which one are you going to take? None of them! Let's pop down an underground tunnel and appear two towns over.
You could also tackle a couple of Gyms in whichever order you wanted. Want to get to Fuchsia City? There are two completely separate ways to get there (and one of them has two different starting points). The same goes for getting to Cinnabar Island.
I appreciate not sticking straight to the drawn routes when progressing through a game. I also appreciate seeing features and possibilities before being able to access them - this encourages exploration. And then there are tunnels and caves which span different locations and can't be confined to a single section of the Town Map.
As far as Legendary Pokémon go, I'm never that keen on apocalyptic stories surrounding them, especially when they're literally true. I'm of the old ilk which just considers them rare and usually stronger than average. It sort of breaks immersion a bit if you're capturing the literal embodiment of time and/or space and using it to fight Pidgey. I also like it when Legendary Pokémon aren't signposted much, which is definitely how Articuno/Zapdos/Moltres/Mewtwo are treated. Moltres doesn't even get its own dungeon, and none of the others have dungeons whose only purpose is to house them - they all contain unique Pokémon and fill a niche even without them (a home for Water/Ice Pokémon, a home for Electric Pokémon, and a home for powerful Pokémon as a post-Elite Four challenge). They're also interesting locations, and not "just another cave with something at the end".
Regarding HMs, I really like how the majority of them (all except Cut) aren't thrust down your throat. You have to seek them out if you want them (you only need Surf and Strength too; you could make do without Flash and Fly). Again, it's exploration, and it gives the player control over their game. If you have a friendly rival or the region's Champion popping up each time you enter a new town, giving you vital new pieces of equipment that you don't even earn, you start to wonder why they even exist in the first place. Fortunately, Kanto avoids this, even in its remake (Johto wasn't so lucky).
And of course, the strip of water down the side of Cinnabar Island full of item-duplicating Pokémon was great. :yum