Well, I'm going to be the voice of decent here and say the ending did not work at all for me in many ways and I am really ticked off by most of it. After spending this long watching the show and characters develop, I wanted the white picket fences for everyone type of ending and it could certainly have worked much better. Here are my main thoughts on this:
First, these characters have been written for 5 years now and have grown in many respects. The way they were in the final episodes though I felt were way out of place. Casey had already changed, he was not the same guy he way at the start of the show and would not all of a sudden acted like he did just for the final mission when the General wanted the "old" Casey. There was no "old" Casey, he has a family now, his daughter and his new surrogate family with Chuck. Yes, he did come around when Morgan confronted him, but that is not the point of him being forever changed already by the last 5 years. While he was off to go after Gertrude and win his true love to be with, he still would've come back to be with his daughter and just told Alex he would be back with her in tow.
Second, Sarah had her memory wiped by the defective Intersect, OK fine. Chuck and crew agreed to destroy the project because they knew others would keep after it and would get a perfected version eventually given enough time. But, they left out the fact Chuck's Dad was the creator of the project and all the knowledge Chuck and his mom had. Are you telling me with their skills and knowing everything over the years of how it works they could not create another Intersect of their own that would work too? I think that would be much better in seeing Chuck nearly kill himself making the grand masterpiece his Father had started. He could've used it not just for himself, but also Sarah to restore her old memories. After all, this was who Chuck was, an expert at programming, not a real spy like Casey or Sarah. Then, they could've destroyed their work and underground HQ at the Buy More like they wanted.
Third, the whole memory wipe, not remembering and starting over has been done countless times and done on Star Trek, specifically Voyager. When I heard about the happy/sad ending I had a dreadful feeling this would be something they would go for given Robert Duncan McNeil involvement with Chuck. I swear no one can come up with anything good anymore and why not give fans the perfect happy ending otherwise? This guy was on Voyager and they did a show just like this which is where I am sure he got some of it from. They even tried the whole falling in love again thing too. It just feels lazy and cheap to me since I have seen this before several times.
Fourth, Morgan and Alex just got a brief "we're moving in together" and that's it? Knowing Casey and how conservative he still is he would've made Morgan put a ring on that finger. I'm sure Morgan even wanted to and this felt very rushed and just tacked on like most of the last 15 minutes of the show. Morgan has grown too and is ready to give up the bachelor pad he and Chuck started out with.
What did work for me? Ellie and Awesome was fine the way that was handled and so was Jeffster, but that's it. They needed the whole last hour just as a goodbye without any missions. Too much of it was rushed and not enough time given to each character. After all this time, I thought it would be a lot more ironic and funny if they all had suburban homes and lives and you got to see a taste of that like a 1 year later flash forward. Can you image the fun they could have with Casey being a home man, you see him all suited up looking like he is going into combat and he says something like "It's war Chuck! I've defeated terrorists and hundreds of bad guys, but I just can't seem to win this battle. I've got ants Chuck, those damn things just won't die!!" You get the point, they could've done all kinds of fun things to end the show on a high note and I feel really cheated after all this time to end it like they did. For me, Chuck was never a serious spy show, it was more a modern A-Team and that is how it should have been kept.
Personally, I really don't see seasons 4 or 5 adding hardly anything to the show. I prefer to think of the way season 3 ended as their last and call it done.