Criticism of the comic aside, two party system is still definitely undesirable. I believe it is a side effect of first past the post voting. What we really should implement is ranked choice voting. It gets rid of the dumb "voting third party is voting for [opposite party]" argument by letting you vote for who you want guilt-free and falling back on your lower-ranked votes if #1 wasn't popular enough.
But you know, this will always meet resistance because politicians would lose their jobs for implementing this.