The only real problem with the San Francisco flag is the use of metal-on-metal (argent, a border or, in heraldic terms; 'yellow on white' in normal English), and in fact argent on argent with the motto. The 'San Francisco' label is pretty silly too.
Fix the colours, use a proper heraldic phoenix, remove the name and it could be an incredibly great flag. Heck, or, a phoenix enflamed proper, in base a scroll gules, thereon the motto 'Oro en paz, fierro in guerra' or would look pretty sharp. Could stick with argent instead of or, if one wished to look more like the current flag.
Fix the colours, use a proper heraldic phoenix, remove the name and it could be an incredibly great flag. Heck, or, a phoenix enflamed proper, in base a scroll gules, thereon the motto 'Oro en paz, fierro in guerra' or would look pretty sharp. Could stick with argent instead of or, if one wished to look more like the current flag.