2 weeks back I stayed 3 nights at Sotetsu Fresa Inn Kyoto-Hachijoguchi, then 4 nights at Marikoji Machiya.
Arranged my itinerary so that those days when I needed to take trains out of Kyoto, I was staying at Sotetsu Fresa Inn, and then when I'm just exploring Kyoto, I'd be staying at the machiya.
The machiya was expensive for just 2 pax, but it's a really nice experience. The tsuboniwa garden was a joy to gaze at every morning and evening while sipping tea/coffee. It looked to be quite inaccessible on the map but we had no issues walking to/fro the 3 subway stations (Shijo, Karasuma and Kyoto-Kawaramachi). Walkable to Pontocho, to Nishiki Market, heck we even walked from machiya to Kiyomizudera

Highly recommend Machiya Inns if you have the budget to spare.
Sotetsu Fresa Inn Kyoto-Hachijoguchi is just a regular business hotel (I'm a member of the chain, and I got cashback - in cash - when I checked out), but its rather new, with Lawson just around the corner. Easy to get to from the station too. Single rooms just perfect for solo travellers. Great location if you wanna stay around Kyoto station area but didn't want to spend too much. I find their prices very reasonable if you book early.