edit: There are multiple Pokemon which come and go due to limited time events. Thus the list of which Pokemon are available right now vs in the past is gettingalways going to be a bit out of date. I do not have time right
Also, trading with other players is now to update itpossible, butmaking it a lot easier to get certain Pokemon you missed.
A lot of previous legendaries are obtainable via the 7-day research reward, or coming back into legendary raids. Also, trading is now a thing, making it a lot easier to get everything you missed.
The only ones you currently missed are via special quests. These quests should have been picked up (but not completed) in a certain time period. Rewards for those were:
- Mew
- Celebi
- Spiritomb
- Meltan (but obtainable via a Mystery Box)
There were multiple limited time Pokemon, mostly legendaries. It is currently not known if they will return (all of them or a select group). These Pokemon were:
- (Shiny) Lugia
- Articuno
- Moltres
- Zapdos
- Raikou
- Entei
- Suicune
- (Shiny) Ho-oh
- Delibird
- Groudon
- Kyogre
A lot of previous legendaries are obtainable via the 7-day research reward, or coming back into legendary raids.
Currently there is another legendary active, Latios/Latias (and shiny Ho-Oh), so be sure to catch that one while it is still possible. Also Mewtwo is available through Ex-raids at this moment in time.
The legendary birds (Articuno, Moltres, Zapdos) were twice catchable. First a week per bird, then about another month where all 3 birds were available at the same time. Now Zapdos is available by finishing a research quest on 7 individual days. Moltres was already available. Articuno will be available in June.
Another 'issue' might be the special hats for the Pikachu family. At specific moments in time they were catchable/hatchable with a different hat.
One other thing that might be annoying is that there are regional Pokemon. For example, Farfetch'd is limited to Asia only. However, there has been an event where it was catchable for 48 hours worldwide. You can still catch Farfetch'd in Asia, but not so soon in your hometown (if not located in Asia) though.
The regions of Seviper and Zangoose are switched right now. Catch the one that should not be in your location!