This likely is way far away from the area you are seeking, but downtown San Diego has several SROs that may not be beautiful but IMO are nice enough studios for short term stays if they are still accepting people on the short term. I stayed at the J Street Inn
Affordable Housing SD and was very happy with my experience there - at the time that I was there (it was several years ago) you could go week to week and it was app. $200/ week - it's likely gone up, but as it is targeted to low-income persons/ affordable housing i would assume it's still pretty reasonable (wasn't able to open the "2008 rates" on their website). But it does also seem to be advertising staying there for "long-term" housing needs now so maybe things have changed? The J Street is right across the street from The Harbor Club, the Marriott, and other luxury hotels so I would hardly call it a shady area.