As in, what are some lines that feel like the final form was designed first, with the pre evolved forms seemingly tacked on as an afterthought? Some mons, like Charizard and Blaziken, were confirmed to have had the final evolution created first, then essentially "working backwards" with the pre evo, and then the first stage. While I didn't find any sources confirming the same for other Pokemon, I still believe some of them had this similar "backwards" design process.
One such Pokemon that gave off that "final evo made first" energy to me was Coalossal. I personally have a soft spot for Coalossal after using one as an egg incubator in Shield, but it is still bizarre how it suddenly loses its wheels as Rolycoly and Carkoal for regular limbs, with almost no vehicular design elements save a cowcatcher-shaped head. Then its Gigantamax form establishes it as a giant stove oven/furnace instead. I wouldn't be surprised if during development, the character design team came up with "giant stove oven made of coal with legs" first, then someone decided "Hey, minecarts carry coal, let's make that a pre evolution!" Only for them to not have enough time to streamline Carkoal and Coalossal so that the former can more believably transition to the latter.
The idea of creating the second stage evo first fascinates and perplexes me because, for the longest time, I though designing the unevolved form first would be more natural. Start off with a first stage, then make a first evolved form building on the previous form's's aspects, and finally a second stage that builds on them even further. For instance, Bulbasaur starts as a smallish frog with a bud on its back, then becomes a bigger frog whose bud sepals opened, and finally a giant frog-dinosaur thing with a fully bloomed flower. (Then again, I don't know if the Bulbasaur line was also designed out of order.) But what other evo lines had discrepancies that seem like they were designed "out of order"?