Whether you know or not, National pokedex is a term starting to appear since gen 3. According to it's meaning, National Pokedex should include all Pokemon generations. So for now, 802 Pokemon is recorded in the National Pokedex. However, the truth is none of the Pokemon core games involve all Pokemon generation. Instead, they have Regional Pokedex to replace National Pokedex.
Kanto: gen 1
Johto: gen 1 + gen 2
Hoenn: Part of gen 1&2 + gen 3
Regional Pokedex doesn't display their effectiveness in gen 1&2 as gen 1 is the first gen and gen 2 involves all Pokemon in previous gen. In fact, gen 3 is a completely new generation to gen 1&2. You can't capture all Pokemon from previous generation. That brings out a question: Could I capture all Pokemon when gen 3 comes out?
As we confirm that legendaries appears with timeframe, there could be a possibility for normal Pokemon as well. Do you acknowledge the rumour about disappearance of gen 3 ghost type Pokemon? This is not totally unfounded. Let's say if Niantic releases all generation, the spawns of Pokemon will be in a mess. Hence, removal of Pokemon spawn is necessary for further generations.
From now on, there are several standard of spawning Pokemon.
3. Season & Temperature
5. Regional Pokedex
Those adjustment on spawn of Pokemon may cause inconvenience to players. Therefore, you should hurry up on catching Pokemon which will not appear in gen 3. No one is faulty in this case. You should ensure you've got enough candies for evolution or power-up beforehand.
Don't worry guys, we still have raids, egg/buddy system and maybe trading in the future. And just to remind you this is likely to be implemented very soon. Time to get ready for your Pokemon team!