@MarMarcin Even though mods are third-party content, EA deliberately made them easy to install and use because the company understood that players would enjoy their games more if they could install mods and custom content. That's why mods go into the game folder, rather than program files—EA patched in this simpler setup in 2010. But if you don't want to use mods, I won't mention them again. Just understand that without them, many of these problems you're seeing will appear again, sooner or later.
(By the way, Overwatch doesn't make the game run faster by itself, although it does clean up errors that can slow things down. It's almost always used with ErrorTrap, and together, they help prevent the save from becoming so corrupted over time that it's eventually unplayable. So you might not notice a difference, exactly; it's just that your game wouldn't slow down and glitch out after a couple of generations.)
Anyway, I'm not surprised that Bridgeport is giving your problems. The EA version has routing issues, and sims also tend to get stuck in elevators and the blacked-out sections of apartment buildings, which is where non-player controlled sims go when they're not supposed to be doing anything else. Bridgeport is not as poorly made as Isla Paradiso, but you still might need to rebuild or repair sections of it to make it run better. I'm not sure where the other errors are coming from, but they sound like typical EA glitches to me. For example, the game loves to give out free cheap cars whenever an inactive sim needs to go somewhere, and those cars just build up over time unless they're removed.
If you save your sim family to the bin, start a new save, and place the family there, the connected vacation worlds that those sims have visited will disappear just like the old homeworld does. So the tombs will all be reset. I don't actually know if the game will "remember" which opportunities the sims have completed, but you could always test and find out for yourself. One possibility is that a sim who has completed certain adventures won't be able to do them again, but another sim will.
As for the store content patches, they're no longer offered through the launcher because they're part of the program files for any player on patch 1.69. This thread explains what to do about it:
https://forums.thesims.com/en_US/discussion/comment/16341942/#Comment_16341942