It is logical to not see Anna as the Queen.
All the films combined (Frozen, Frozen Adventure, Frozen Fever and Frozen II) without the intros and the credits have a combines runtime of approx. 208 minutes.
Anna is introduced by Kai as Queen Anna 3 minutes before the end of Frozen II, so she is Queen for 3 minutes in the entire Franchise.
Elsa is introduced by Kai as Queen Elsa 20 minutes into Frozen, 18 minutes without the intro.
208 minutes runtime minus 18 minutes before Elsa was Queen and minus 3 minus Anna has been Queen means that Elsa has been Queen for 187 minutes through all the films while Anna only has been Queen for 3 minutes.
This means that through all the films, Elsa has been Queen over 60 times longer than Anna has.
So naturally we still see Elsa as the Queen, even though the entire franchise ended with Anna being Queen.
This will surely change a lot when Frozen III gets released and after Frozen IV Anna will probably have been Queen longer than Elsa.