Misato ending only occurs if you talk to Shinji EVERY WEEK! Plus you need the "Campus Route" for marriage endings. Which requires you enter the "Pathos Route".
I played Pathos Route and its pretty much impossible to access Campus Route. Maybe the game is bugged?
You can see the most well-written guide here (but it is on Russsian):
You must be registered to see the links
Rough translation of some crucial parts by non-native English speaker
- There is a hidden parameter in game, so called "independence", one of the most important in the game, defines the route. From the very first Sunday is 500 pts. During the game, it can be decreased/increased by: -1 for synchrotest, -1 for combat training, -10 for illness, -20 for the defeat of friendly Eva in battle, -30 for going berserk; +1 for attending school, +1 for free time with friends, +5 for vacations (only once a month), +5 for every ten visits to the school club, +5 for special events with girls, +10 if you managed to avoid going berserk. Also, it can be increased from some of the events of the Pathos route, such as a beach cafe and survival training.
- To move from the 20th chapter of Thanatos route to the 21st chapter of Pathos route or from the 20th chapter of Pathos route to the 21st chapter of Campus route you should meet two conditions: the independence parameter must be above 550 pts and Eva-01 in the battle with Zeruel must not go berserk. Using berserk during the battle with Zeruel will provide a transition to the Thanatos route. From the 21st chapter, the independence parameter loses its importance - we will play the same route that starts from 21st chapter till the end of the game. The exception is the 24th chapter of the Campus route, where you will have a choice: continue the game on the Campus or return back to Pathos