TheFork users who ate in Berlin have said really good things about Batumi (Gasteinerstrasse), Don Quijote and Gasthaus Kater Alex. Maybe you should give them a try!
Some of the more popular Omelette restaurants that offer vegetarian options on their menu in Berlin according to TheFork users include:
Batumi (Gasteinerstrasse), with a 9.4 rating
Gasthaus Kater Alex, with a 9 rating
Café Bar Pirouette, with a 8.6 rating