Are Theodore and Amy meant for each other?
That's what the ending may me think of.
Maybe the softwares, her friend and his girlfriend (Samantha) helped them getting closer to eachother.
Maybe the fact both the OS left made Amy and Theodore realise they had eachother, and always had. They were just too busy with their respective computers.
They are great friends, they don't judge eachother, they've always been supportive to one another, and they're now both single. I say the ending is an opening to a new loving (and real) relationship.