Steep & Close

The only city that's missing now from Homer's sequence is Pylos itself. We've already established where not to look: it's not modern Pylos and it can't be south of Filiatra or north of river Neda. It shouldn't be too far from the sea, though not so close it would be vulnerable to attacks.

When Telemachos arrives with his ship, Homer writes:

Something like this?

Odyssey Book 3 line 3-4 Barry B Powell
Odyssey Book 3 line 439-440 Barry B Powell
Odyssey Book 3 line 299-306 Barry B Powell
Odyssey Book 3 line 350-351 Barry B Powell

The Ithacans came to Pylos, the well-built city of Neleus...

Nestor is unable to provide any information about Odysseus, so after Nestor and Telemachos talk on the beach about the returning of all ships from Troy, Athena (Mentor) thanks Menelaos for the wise words...

...and then the sun went down and the darkness came on.... ....But come,... ...we may make a drink-offering to Poseidon, and to the other gods, then take thought of sleep. It is time for that. The light has gone down beneath the darkness. It is not right that we sit long at the feast of the gods. We need to get on our way.

Then the horseman Generian Nestor led them, his sons and sons-in-law, to his beautiful palace.

Mentor heads back to the ship, while Telemachos stays behind with Nestor and his company.

After the sun goes down they walk to the palace. On December 10th twilight would have taken about half an hour. There would have been no moonlight since the moon was waning and rising late. The palace has to be near the sea, be well-built, have a good view over the surroundings and lie on or against a steep hill or mountain.
There happens to be such a place close to Kalo Nero.

And not unwilling, they sped over the plain, leaving behind the steep city of Pylos.

We're looking for a well-built city. There would also have to be a strategic view over a considerable part of the area and therefore we can expect it to be high up on a hill. Actually, we can be quite certain in the case of Pylos, because when Telemachos leaves with car and horses accompanied by Peisistratos, the son of Nestor, Homer specifically states:

Or like this?

Pylos

Arene

Thryon

Aipu

Kyparisseis

Amphigenia

Pteleos

Helos

Dorion