I always found the finale very silly. It was sad, yes, but stupid. Puss has never before been seen to harness any special power, except in the ones where he is given them, and it usually only lasts a day before they get taken away again.
I know why they had Puss leave San Lorenzo though: The movie.
However, I have a better solution than having the whole series basically become pointless because none of the characters remember it anyway: have Puss choose to leave.
Puss only stayed because he had to, after he broke the spell protecting it. And yes, he learned to love it there, falling in love with Dulcinea and making friends with the orphans and other characters. But, I feel it should have ended with Puss fixing the spell, and then choosing to leave. Puss loves the town, yes, but he is needed elsewhere to help keep justice other places. After the spell is fixed, have Puss realise that although he'd like to stay, he simply can't as he can't be a savior in one place. Have it end with the same emotional goodbye, maybe promising to visit, and then have him leave on his horse.
We cut to the thieves' market, where Puss is getting ready to continue his journey. However, as he is about to run off into the sunset, a mysterious someone drops a note onto his hat before running off again. The note has nothing written on it, except a rock. You know that rock where Dulcinea met Esteban, the star she could wish on? That is what the sketch is of, with Dulcinea sitting on it. A few steps away, it shows a drawing of Puss staring up at the same night sky. This is a clear indication by Dulcinea that, whenever they miss each other, Puss just needs to look in the direction San Lorenzo is in, and stare out, imagining Dulcinea on the rock, staring up at the same sky.
It cuts to black, showing text that says 'one month later.' Puss is sitting by a campfire, alone, when he suddenly imagines Dulcinea. He smiles, and glances toward a certain direction where San Lorenzo is. It then quickly zooms in, showing Dulcinea sitting on the rock, staring out, with her paw out, like she is touching a wall. It cuts back to Puss, who holds his paw out. The screen is then cut in half, showing both, as their paws touch. Then the credits start rolling.