Both GT frames are solid. The difference is in the components. The Series 3 utilizes Shimano Tiagra components and the Series 4 is equipped with Microshift.
If the budget is not going to be burst, than I would go with the Series 3. Microshift is kind of clunky shifting. Both bikes will be fine for you but I would simply go for the Series 3 based on my experience between Tiagra and Microshift.
It would be extremely difficult to tell you which bike is better between the Fuji and the GT. They are both good bikes. It is just a matter of preference. The GT Series 3 does have a better drive train though. Tiagra is one level up on Shimano's groupset. Sora is still good but Tiagra is just a step above.
The GT is more traditional/race oriented while the Fuji is more of an endurance style road bike. Again, they are both good bikes and it is just a matter of preference. Personally, I would go with the GT Series 3 as it is less expensive than the Fuji Sportif 2.1 and it has better components.

 

As far as the frames go, I'm pretty sure that, except for the paint, the 3 and 4 are the same. It used to be the case that the 1 and 2 (and the 1 was only available in the US through Performance) had a slightly lighter and more aggressive frame, and they utilized internal cable routing for the shifters. Different headset and BB, too.

But it's been awhile since I kept up with what GT was doing.

 

I own a 2012 GT 4 that serves me very well both for commuting and recreational riding; I average about 130 miles a week. Given the $600 budget you mentioned in your other thread, I would go with the 4 and use the difference for accessories. Or, if you already have everything you need initially then go for the 3, as it is a much better drivetrain.

 

In 2012, the 4 was Sora. They still had the entry level 5 with a mix of 2300/Microshift drive components. The 2014 GTR 4 is now what the 5 was, with a mix of Claris/Microshift. For a beginning rider, I think Sora is fine, although Tiagra is a step up.