Ok so time to brainstorm some ideas!
Doge's Palace: Reduce the extra base yields it provides somewhat. Remove the +GP production, tourism, and anti-spy elements. Add "Whenever borders expand in this city, gain +15 food scaling with era" (the Doge originally had full control over Venice, and as a City State the objective was always to increase the wealth of the city itself, represented as more territory and more productive people)
The Great Council: Unlocks at Trade. +2 science, +15 science scaling with era when a building is built in this city (The Great Council of Wise Men took control of all legislative duties in the city. As members of the noble houses, improving the power of the upper class was paramount, represented as more industry and cutting-edge tech to capitalize on)
The Council of Ten: Unlocks at Civil Service. +10 production, +10 defense. Advanced spy actions can't be taken in this city. (The Council of Ten had unprecedented executive power in comparison to the rest of the government. Originally intended as a temporary stopgap against insurrection, the Council of Ten expanded to protect against corruption, espionage, and even started to take on basic legislative duties because they could actually get things done)
Murano Glassworks: Unlocks at Metal Casting. +4 production, +4 culture, +4 science, +4 gold. Doubles all luxuries in this city. (Venetian glassblowers were famous across Europe, and because none were allowed to leave the city, very few other places were able to match. Byzantine refugees with craft skills were taken in, which cause widespread learning and art, known as the Renaissance)
St. Mark's Basilica: Unlocks at Theology. +10 faith, +10 culture, and majority religion pressure emanates at double speed (the Basilica was the center of the state religion, and unlike other Catholic nations, Venice controlled its own church for most of its history. Also Venice needs help with faith and spread in-game)
Venetian Ghetto: Unlocks at Writing. Has a Merchant slot. Trade routes to and from this city provide +3 gold for both parties. (The Ghetto was home to one of Europe's largest and most successful Jewish populations, with familial merchant connections across Europe and the Middle East.)
Venetian Arsenal: Unlocks at Sailing. +5 production, +40% production of naval units, Naval units built here receive +15xp (the Arsenal was a mass-production system which resulted in quick building and repair of ships but also enabled better ships to be built and the expertise to build them to be easily taught)
Gondolieri Guild: Unlocks at Guilds. +15% GP production, and all Venetian UBs provide +2 tourism. (originally, Gondolas were used as the main mode of transportation around the city, and were covered for privacy of their high-class passengers. Nowadays they are one of the main tourist attractions for the city, which is why the covers have been removed)
Grand Canal (we can rename the World Project right?): Unlocks at Engineering. +4 production, +4 gold. All GP improvements worked by this city provide +3 food, +3 culture, and +3 tourism. (the Grand Canal provided easy access to the inside of the city, increasing productivity as goods could be unloaded directly to their destinations. This has allowed for many amazing structures in a dense area, causing cultural intermingling and nowadays tourism. The density is represented with food.)
Just some ideas. Obviously the yields need to be balanced, especially against the hammer cost of the buildings. I would expect these buildings to cost about as much as a National Wonder.