Although I typically favor preservation by timely, routine maintenance along with replacement/upgrades that are first, thrifty and second, actually an improvement to the machine. It's very easy in this business/hobby/passion to be guilty of putting lipstick on a pig. That is not to imply any sort of poor thinking when one wishes to experience Ultegra instead of old Sora. Pretty logical, in fact, as the kilometers tick by day after day. I spent about 25 minutes doing a little web-surfing research as I thought about your situation, and here's what i think:
This Giant freehub body is 11 speed, swap-able with your current Defy hub and costs a reasonable 20 pounds. I doubt your rim is trashed and it can be made rideable again. One consideration may be the degree of wear on the rim's braking surface (though i didn't see it specified, it's likeliest your 2-3 year old Defy 3 has Tektro caliper rim brakes). The Giant SR2 rim has a machined groove around its circumference which is a wear indicator common on rim-brake rims. The rim's useful life is about done if this groove is worn smooth. I mention this because, it may be a better value to obtain an entirely new wheel that comes with an 11 speed hub. The repaired, old rim becomes your backup.
There are several listings on Ebay for new (and used) Ultegra 6800 groupsets. They're running around $700 with shipping costs considered. Obtaining just the derailleurs, shifters, chainset, and cassette (that's the minimum of components needed going to 11 speed) will run into the neighborhood of $400. Neither of these options consider the cost to put these components on and get them in tune.
According to Bicycle Blue Book, a 2016 Giant Defy 3 is valued somewhere between $2-300. A high quality groupset represents the greatest chunk of a bike's consumer cost, so I'm not trying to point out the discrepancy in the bike's value "as is" vs. new component cost since I'd be willing to venture that in a cost analysis of a new bike's price, the components comprising the "groupset" represent 2-2.5x the cost of all else that makes up a complete bicycle. That said, this discrepancy does give one pause when considering the "upgrade."
Finally, note that a 2018 Giant Defy Advanced lists for $1685. This gets you a carbon composite frame, disc brakes, and the 10 speed Shimano Tiagra Groupset, which should be very close in quality and performance to Ultegra 6800. Interestingly, if it happens to be Tiagra 4700, this model number utilizes the same shift actuation ratio as Shimano's 11 speed groups. Relevance here is that, presumably, one could do a future upgrade to 11 speed Ultegra a bit more conservatively--piecemeal, if you will--since the 4700 Tiagra shifters would correctly control 11 speed Ultegra derailleurs that you could pair with an 11 speed Ultegra cassette when the Tiagra cassette wears out. Conventional wisdom states one wears through two cassettes (and at least 2 chains) before the chainwheels need replacing. If you keep to your current bike mileage pace, in a little over 2 years time, you'll be fully Ultegra on a bike whose material and geometry remain in the upper tier of the bike world. In this case, buying new at a well-defined cost(and acquiring the benefits of warranty and one or two free services for the new ride) far outweigh the expenses and risk of this proposed upgrade.