To clarify, PMD and Pokemon Ranger are spin-offs, not crossovers. And the terms "spin-off' and "crossover" are the same but different. Sounds confusing?
Spin-off games are games outside of the main series. They may, or may not, follow the same style, gameplay and even timeline of the main Pokemon games, but they're Pokemon games, none the less, but with elements not found in the main games. Take PMD for example. One thing you'll notice off the bat is that your character is a Pokemon, not a Pokemon trainer, which especially appeals to fans who want to know what it's like to get through a Pokemon game as a Pokemon, not a human.
Crossovers are like a sub-type of a spin-off game. They have the same attributes as spin-offs, but have one unique element that stands above the rest: It combines elements of another game series. Pokemon Conquest is a great example of a crossover. It combines the Pokemon creatures, moves, types, etc. of the Pokemon series, and the chess-like strategy, the use of kingdoms and the kingdom system, and the war/peace system (if there is one) of Noabunga's Ambition.
As for the question? As long as Nintendo and Game Freak know what they are doing, they can either make their first Pokemon crossover their last, or basically, just their first of many (or few.) If the companies feel that crossovers won't work for them, they can cut the crossover idea, but most of the time, it would only be cut off temporarily. There will be times when they think that a crossover would boost their sales, fanbase, community, and even all three of them.
So, it depends on the aforementioned companies if Pokemon crossovers would last or not.