Kanazawa or Nakasendo trail?

I am considering a visit to Japan for May. Definites on the list would be Tokyo and Kyoto. Instead of going straight from one to the other, I am looking into travelling via Kanazawa or the Kiso Valley to do the Nakasendo trail. I have about 2 days spare to do this. If anyone has done both, I would love to hear how the two compare and which you think is better.

Kanazawa and Nakasendo are two very different targets. Kanazawa is usually for the garden and castle (and the chaya district and a few others), while Nakasendo is a hike between various post towns. Certainly Kanazawa transport/logistics is much easier, but the two are very different.
Which one is "better" depends on you and what experience you are after.

I've been to both several times but now tend to head toward the old Nakasendo post towns over Kanazawa just because I now try to avoid the ever-increasing tourist crowds. That said, I think you'd get more out of a 2-day stop in Kanazawa than spending time along the Kiso River.

Nakasendo (Kisokaido) has:
Kiso-Hirasawa - lots of lacquerware
Narai-juku - the next town down from Kiso Hirasawa within walking distance
Magome-Tsumago hike with the 2 post towns as end points and couple of waterfalls in the middle
Some of the other post towns have a few buildings here and there but not as preserved as the above 3.
All have old Edo Period buildings strung out along a single street of the Nakasendo.

Kanazawa:
Has the Nishi- and Higashi- Chaya districts, similar to the post towns on the Nakasendo with old architecture.
Nagamachi Samurai district with old mud walls capped by small roofs
Kutani-yaki pottery - shop and watch the potters work
Temple district with "Ninja-dera"
Kenrokuen - two level garden with water brought in from a nearby river
Arts and Crafts Museum & Seison Villa next to the gardens
Omicho Market
Old Castle grounds with some reconstructed buildings - part of the park was closed from the earthquake.

The only problem with Kanazawa is that the train station is off by itself. I select a hotel in the Korinbo area which is in the middle of all the sights and just take a taxi from the station.