Upgrading from 9 speed to 11 speed on Giant Defy 3
On road drivetrains the freehub body was made a little wider for 11 speed to accommodate the extra sprocket (34.75mm for 8, 9 and 10 speeds to 36.75mm for 11 speed), so unfortunately the 11 speed cassette cannot be mounted on your hub.

I believe there may be some hacks to get over this, but I cannot provide any information.

Edit: Some 11 speed cassettes will fit on an 10 speed freehub body, specifically larger sizes where the large sprockets can overhang the inboard end of the freehub body, I believe. 

You could upgrade to the 10 speed Tiagra group which would still be a substantial bump up in performance and reduction in mass.

It could be said that going to Ultegra is not worth the cost as the rest of the bike is still at Sora level. Also, separate groupsets are relatively expensive, and you have to take into account the cost of installation. Very often it's a better idea to simply buy a new, upgraded bike and sell your old one.