If the observers were from the alternate universe, how would sending the child observer and Walter into the future (in their universe) change the plan that occurred in the late 22nd century (suppressing emotion to benefit intelligence)? To me, it does not make sense that the observers are from the other universe.
Obviously observers can enter the alternate universe, as evidenced by September interrupting Walternate's successful attempt at finding a cure for Peter, but generally, the observers interference in the alternate universe seems to be minimal. Further, in the show, the observers seem to be more involved with time travel than with travelling between universes. Is this accidental?
I don't really have a theory as to why they haven't invaded the alternate universe, other than perhaps they want to take on one at a time. One of the observers states that they chose the time period they did because there was a 99.999% chance of success. Perhaps it is simply that this universe at this time is where they concentrated their efforts based on probability.