Kyoto is compact enough that no base is truly "wrong," but where you sleep does shape your trip — mainly through what you get for free at the start and end of each day, before and after the crowds.
Kyoto Station area
The most practical base for a first visit: every JR line, the subway, and most long-distance buses radiate from here, and there's a dense concentration of hotels across every price point. The trade-off is atmosphere — it's a modern transit hub, not historic Kyoto, and you'll commute into the districts you actually want to explore.
Downtown / Kawaramachi
Central, flat, and walkable to Nishiki Market, Pontochō and the main shopping streets, with good access to both Higashiyama and the subway network. A strong all-rounder base if you want to walk to dinner rather than commute to it.
Higashiyama / Gion
Staying inside the atmosphere pays off specifically at the edges of the day — walking Sannenzaka and Ninenzaka's lanes at dusk after the tour groups leave, or reaching Kiyomizu-dera on foot before opening. The cost is a longer trip out to Arashiyama or Fushimi, and generally fewer large hotels, more ryokan and boutique stays.
Arashiyama
Scenic and genuinely peaceful once the day-trippers leave, but the furthest from everything else — a reasonable base only if Arashiyama and the western hills are your main focus, or as a one- or two-night change of pace within a longer Kyoto stay rather than your only base.