Whenever I hear the phrase "Ratchet settles down", it sends shivers down my spine. I know everything needs to have an end, though I'd like to prolong the inevitable as much as possible.
Finding the lombaxes doesn't necessarily mean the end of the story, it can be a new beginning. Maybe things aren't so bright in the new dimension and the lombaxes encountered new threats. And somehow things get out of control (and for some reason the highly advanced race can't handle it), so, right in the nick of time an outsider (we know who) joins them and saves the situation.
This idea may have tons of errors in it, but it's just a simple example of how things can go. I believe that as long as Insomniac wishes to continue the franchise they can come up with anything.