For instance, Masahiro Sakurai, from Smash Bros, initially explained how Rex, from Xenoblade Chronicles 2, was cut from the roster in Smash Bros Ultimate due to time constraints. At first, this was taken a bit... awkwardly, because later he added Byleth from Fire Emblem Three Houses, when that game was in development.
However, when Pyra and Mythra were added, also from Xenoblade Chronicles 2, Sakurai explained how it wasn't possible to have Rex playable with a swappable Blade, due to the Switch's hardware limitations.
Here's what I understood later on: if Sakurai stated that "Rex wasn't added due to hardware limitations", when Smash Bros Ultimate was released in late 2018, less than 2 years in the Switch's lifespan, that... wouldn't have been good publicity ^^;
So yeah, was there a developer's excuse/justification that you only understood later?
It's pretty easy to understand. Ultimate's roster was finalized in 2016. Sakurai didn't play Xenoblade 2 until 2017 or after - it was too late to add him to the base game.
Nintendo decided the DLC for Smash, not Sakurai. Nintendo must have felt they wanted to promote an upcoming Fire Emblem game when the DLC was decided on.
Maybe Nintendo suggest Rex as well but Sakurai said movement wise it wasn't possible, but Pyra/Mythra were.
About Sakurai not deciding the DLC... I don't think that's entirely true. Most weren't his choice, but a few -like Joker and Terry- were.
http://www.nintendoworldreport.com/news/48860/sakurai-issues-statement-on-smash-ultimate-dlc-characters-selected-by-nintendo
Here Sakurai said the list of possible DLC characters was made entirely by Nintendo. Sakurai just told them whether a character was possible as a fighter. Beyond that who knows how much input he had.