The easiest way to solve this problem is to lower starting opinion towards the emperor a bit so that the he can't call on so much levies. Keep in mind im talking REALLY MINOR changes. In CK2 i've never seen the Seljuks win that first war.
edit2: Ok they were, but it doesn't look like they were THAT strong at the time. It wasn't so much their military strength that saw their rise, but much so the decline of the byzantine empire(or so I understand it; correct me if i'm wrong).
Doukas starts with +30 bonus to vassal relations because he's defending against infidels, that's already the only thing keeping it afloat with such a terrible ruler. It'd fall apart right away considering Byzantines also have high crown authority. And it does, but after the battle. However, I don't see the Seljuks turning it around because they also break apart with rebellions after Alp Arslan dies. Way too many rebellions in the game already, Muslims need something else.
As for Ottomans, the power vacuum sure helped at the start but after that, they repeatedly defeated multiple crusader leagues, all Balkan states, everyone in the Middle East. In fact, only Timur was able to deal a serious defeat upon them (and he did that vs anyone he fought, one of the most exceptional cases in history) during CK's timeframe. They also were the closest thing to a New Rome: Never again Mediterranean region saw another dominant world power that encompasses most of its shores with a 'Pax' effect.