This article sorely under-represents San Francisco. Nevermind that summers are notoriously the coldest, foggiest time of year (...ever wonder why tourists are walking around wearing fleece SF jackets they bought at the wharf? Or the famous Mark Twain saying, "The coldest winter I ever had was summer in san Francisco."?!) but to suggest in-symmetry for a massage is so random. Great establishment I'm sure, but it's in Potrero Hill, no where near the other places mentioned, and unless you're staying in the Mission, Dogpatch, or Bernal, it's not a super close cab ride by any means.
As a ten-year 'local' I can say there's so much in SF to discover! Depending on what you like, I'd avoid the touristy Peir 39 and Wharf altogether. You don't go on a honeymoon in a fantastic destination to meet people from absolutely everywhere else except where you're staying. A few favorite places (most are accessible via cable car, "themed" trolley, bus (for the real adventurers) or by walking. City Hall is uncommonly gorgeous, across the street The Asian Art Museum, Hayes Valley shopping (shoe afficianatos rejoice), or dining: anywhere from the quaint Stelline, or the community dining German feast at Suppenkuche(sp?). Donr forget the cozy coffeehouses, French (chain?) on the corner of hayes and Octavia...or the awesome happy hours and sandwiches at momi toby's (cash only). From there, test your hill climbing skills for the reward of Alta Vista Park, otherwise known as "The Painted Lades" or opening scene for the sit-com Full House. Cab it, walk, or snag a bus (22Fillmore) to the jazz district (Yoshis)or famed "The Fillmore" with museum of posters upstairs under those magnificent purple chandeliers. Hit up a Korean grill (cook your own meal) in japantown, or mosey towards popular local haunts like The Grove or Molly stones for picnic fare. Keep walking fillmore St or bus it over the hill to awesome views, and cow hollow/marina dist. Take a stroll or jog along the marina green, soak in the sailboats and dog lovers at the nearby park or presidio (grab a coffee at the hidden gem, a small coffee house tucked in the corner overlooking the water.) taken Chrissy Field (The Warming Hut) and views of the GG bridge's underbelly for pictures that your friends will think are photoshopped they're so gorgeous! Check out George Lucas' massive ILM campus if you're nostalgic for his work. Grab a burger at Liverpool Lils and venture toward north beach's little Italy if you want to walk among both tourists and locals (Stinking Roses) but don't dine at places on Columbus where they rope you in on the street; they're overpriced and full of tourists. Take pics of Alcatraz from Lombard St ("the crookedest street"), ponder the high real estate while you gaze upon The lighted Coit Tower, on of the places my fiancee and I first "knew" we were madly in love. If you're a pizza person, North Beach Pizza on Green St is for you. Are you a writer, poet or into the Beats? You won't want to miss Kerouac alley where Kerouac and Ginsberg walked, read and started a movement. Get a beer at Vesuvios, throw a nickel in the Italian opera jukebox at Tosco's and have a brandy hot chocolate...perfect unwind to the SF chill. Get on a cable car (buy a visitor pack for 3 rides for $11, instead of $5 one way!) and head over the beautiful tree-lined Hyde St, which you'll recognize from numerous movies,including Heartbreak Kid. You could grab an ice cream on the corner of Hyde/Union, or you could jump off at the corner of Sacramento(?)/Hyde and take in the cable cars and locals at NOOK. Whatever you do, really take in a neighborhood or several, remember it's one of the friendliest places in America, so don't hesitate to ask people for their opinion. Do your best to simply ignore the homeless, they're aggressive...cold as it sounds, they will suck your energy (and money) if you engage them even a little bit. And remember, renting a place is a good cheap alternative, but one of the treasures of staying at a hotel is the convenience of a conceirge, in house gym or spa. Unless you know the house or they've left you with hospitable local ideas, you might just feel like you're on your own without the convenience of nearby cabs or the compass of a dedicated hotel staff.
Enjoy our magical city!!