Well, I'd imagine they would be caught off guard by a few things, or at least be surprised:
- That the fairy-type exists now, though seeing that it's part of one of Pokemon's most well-known game mechanics (types, duh), they'd probably adapt to this one eventually. They might also be surprised how well fairies do against dragon-types.
- All the new designs. I figure that they'd either dismiss them all, or be more open-minded and enjoy them.
- 'Dexit'...yeah, I'm not going down that route. Moving on.
- Some of the 'generational' battle mechanics, such as Mega Evolution, Z-Moves, and Dynamax/Gigantimax. I feel like for the former two, our recently awoken 90's Pokemon fan might question why those mechanics were only in one generation once they learn more about them, and for all of the mechanics in general there could be some complaints about power creep. On the other side of the coin though, They'd probably still be fascinated by these mechanics regardless.
- Overall, that the franchise is still going strong after 20-something years. I could be see them being surprised that the series has had as much staying power as it's had and maybe even pick up right where they left off.