There can be a number of theories but I think the primary one is because it would have few viewers, certainly not enough to make the show profitable.
TV shows are a conveyance for advertising - it is meant to be a profit center, and cannot be just ART .
Ideally every television show's advertisers want millions of viewers each week, something that is difficult if the audience is expected to reboot their thinking at every return from a commercial.
"Are we in universe 1 or the alter-1?" is easier to handle than, "Are we in universe 1, alter-1, alter-2, alter-3, or _alter-N?"
The writers would get confused, the actors would miscue which one they were supposedly in, the writers/actors would have to develop/portray different back story and keep them alive (but separate) simultaneously.
All this is a lot of trouble, and would develop a diligent core viewership of art followers who, granted would like to keep expanding the universe until it filled their heads.
But, honestly, the number of viewers dwindles each time the alter-N is increased because, "It's just too damn hard" to make it, to portray it, and, frankly, for the average viewer to watch it.
And every time an audience member leaves, the show's sponsor's pockets gets slightly emptier.
So, they've acknowledged it through dialog that there are theoretically greater than two universes.
However, I think they have kept the universes to two to keep the dedicated audience, and to help the actors and the writers.
movies.stackexchange.com/users/304/wbogacz
You can possibly rectify this with string theory by extrapolating that these two universes are already converging, making it easier to cross between them as opposed to other universes.
This would also explain why they both have so many similarities like the fact that human life exists on a planet with identical composition and that many of the people have genetic equals in both universes.
movies.stackexchange.com/users/3564/Supernatendo
Any more and we'd either be watching sliders (with them unable to get home and constantly moving) or stargate (inevitable hostile universes trying to invade)..
The story simply demands only 2...
movies.stackexchange.com/users/1202/Paul Hutchinson
As I remember, I think that their reasoning came from the fact that those two universes were the closest.
Those were the two overlapping.
To get to a farther universe would be theoretically and fictionally, impossible
movies.stackexchange.com/users/5199/James
Actually, my opinion is a bit anthropic; it's how it is because this is how it happened.
Walter opened a door between two universes.
Most doors only go to two places.
Thus, these two universes are linked because of the door.
One could try to make another door go to another universe, but they never try that; they are pretty much focused on the universe that Peter came from.
movies.stackexchange.com/users/5178/levitopher
I mean according to Walter, there could be any number of infinite universes if I'm not wrong. So why do they only talk about two universes and only one remaining in the end. What about others?
Why is there only a single parallel universe in Fringe?
movies.stackexchange.com
<fringe>
movies.stackexchange.com/questions/2072
movies.stackexchange.com/users/1197/Uday Kanth
You can possibly rectify this with string theory by extrapolating that these two universes are already converging, making it easier to cross between them as opposed to other universes. This would also explain why they both have so many similarities. These two universes are already converging. 
You can possibly rectify this with string theory by extrapolating that these two universes are already converging. This would also explain why they both have so many similarities.