Both of them were picked by Sakurai using the mainline games' concept art. In other words, their games weren't even released by the time they were picked, so assuming the anime, which comes even later than the games, has a weight in the decision feels like straw-grasping, imo.
So their spotlight in the anime is either a coincidence or you've got the reasoning backwards and it's actually Game Freak/TPC/whoever makes the anime that decided to milk whoever Sakurai picked.
The anime should be seen as hints for a choice, not the actual reason for the choice. And even then, the first Pokemon isn't always the one we get, as seen with Litten/Incineroar.
The only character who was chosen specifically because of the anime was Lucario due to his movie.
This is sort of long, but Pokemon speculation is something I've invested quite a bit of time in for each Smash game.
Writers in the anime typically know the highlights of each series' plot from the very beginning, and I do think their decisions have been a strong influence for Sakurai and the Pokemon he chose for Smash.
Take Froakie and Litten for example. Even though neither of them evolved until much later, the writers had thrown in several hints in the first few episodes that they'd be a little more important to the plot than the other starters. Froakie was the only Gen 6 starter Ash owned, which is a huge step up from Chespin, the comedic relief, and Fennekin, the Pokemon whose trainer wouldn't decide what she would do during the series until the halfway point. I also think Ash-Greninja was something they had been planning for a while, since the tradition of making most of Ash's new Pokemon be from the current Gen was kept. Diance was the only Gen 6 Pokemon capable of Mega Evolving, so if they wanted Ash to be able to use Mega Evolution without relying on a Pokemon from a different Gen, making a special Mega was their only choice. They handled Litten and the Gen 7 starters in a similar manner. Popplio was owned by a character who would battle significantly less than Ash, Rowlet (despite being one of Ash's Pokemon) was the comedic relief with very little character development, and Litten was the one who would go on the handle the deeper, more meaningful plots. They had also included Incineroar as one of only three Gen 7 Pokemon in the I Choose You movie, and that's something that they had likely decided on months before SuMo even hit store shelves. There was definitely a stronger push for the Litten line than the other two.
At the bare minimum, Sakurai could've asked, "which starter do you believe will have the most important role," and they should've easily been able to give him an answer.