They skipped it because they would have to make new assets for the baby characters. 2 isn't coming to Switch.There's good reason why they skipped it, Bowser inside story heavily relies on the duel screen set up and can't be realistically be remade without redesigning the game to work on a single screen. Plus it was the best selling Mario and Luigi game.
Partners in Time, however doesn't really use the whole duel screen set up. So it can be remade on the Switch, should they ever opt to do it.