From the best of my memory, Persona 1 and 2 take place in a different timeline. And if everything said in SMT4 is canon, then all the timelines happened - but the difference in this situation is that under normal circumstances a timeline isn't overwritten. In P2, time was overwritten and in P5 reality was overwritten.Maybe I should have said "a very fuzzy canon adjustment" instead of an entirely new canon, but Persona 3 changes a lot of the fundamental rules of the series. Just from the top of my head.
- Adults are not able to use/control personas in Persona 3/4/5, despite Persona 1/2 having villians and party members using them without issue.
- "Normal" persona users are not able to change personas at will in Persona 3/4/5, despite the Persona 1/2 party being able to do so.
- "Special" persona users are able to use all personas, marking them with the "Fool" arcana - indiciating they've started a magical journey.
- Normal people are able to see (but not enter) the Velvet Room, which in Persona 1/2 are located in malls like regular stores. Persona 3/4/5 changes this to a magical space only very specific people can even see.
- The Velvet Rooms in Persona 1/2 have a wider variety of employees (pianist, singer, painter) and they aren't (possibly) powerful otherworldly beings unlike the P3/4/5 cast (Elizabeth and company).
- Persona 1/2 have a much closer tie to SMT via the enemies being classed as literal Demons (that can be negotiated with). Persona 3/4/5 they aren't "real" demons, but manifestations of peoples desires/conciousness/etc.
Even though it's one canon (and Persona 3 does reference characters from Persona 1 and 2) - the games are very different on nearly all levels; gameplay wise, huge changes to the narrative, changes to all of the themes and world building.
Persona 1 and 2 feel very much like SMT games, where as Persona 3 forward feel much more like their own thing (with a few homages along the way).
It would be sidesplitting if Persona 6 was a return to Rumor Power.