When playing through the official story line, I found out that you can take those extra maps made by users and place them into the actual story.
Depending on the map design itself, certain maps won't make sense while others will fit perfectly.

By going to "Valve\Portal 2\portal2\scripts\vscripts\transitions"
These files handle the transitions for each level. If you want to add/edit/or remove any maps, just edit the file "sp_transition_list.nut"
Scroll down until you get to "MapPlayOrder"
Here you can add/edit/or remove any custom map you like. As far as I know, you can not change the first map(maybe of each chapter, not sure).

So anyone who wants a longer game, this is how to do it. The tricky part is finding great fun maps to fit with the game.

Custom maps disconnect at the end so it won't continue to the next map after a custom one for the most part.

Well I just tested it out with one of the custom maps and it worked fine. I'll try to test some others to see if they cause any issues.

edit: It overrides the disconnect. I beat this map recently and saw the Thank-you message. However when I placed it in the map list, that screen never appears. I have a feeling it only disconnects because there were no other maps found.