Maybe Byzantium as a state could automatically have reduced vassal levies overall but a higher tax rate, to be able to support the tagmata.
I could edit the theme system law to only have two options, Inactive (With the massive levy/tax penalty for late game Byzantium) and Active (Which gives nothing). If I restore the 0.8 maximum levy command for viceroyalties then Byzantium would probably have the same troops numbers, but with half of them mercenaries. The average maximum levy for Byzantium is around 40,000 men, so if I reduce it to say 30,000 men and then add in the four tagmata (Which are 4,000 men each) I'll end up with 56,000 men, which isn't too far off the mark, but is still very high.
The Byzantine Empire might be very OP in 1066 though, because it had around 40,000-50,000 tagmata troops (6,000 from each of the main tagmata, 4,000 from two new tagmata, and the rest from the foreign Hetaireia regiments). Then again, Byzantium only lost in 1071 because half of Romanos' 40,000 men abandoned him. He could very well have won, or at least forced Alp to turn back. The Byzantine army actually retreated from Manzikert in good order, it wasn't the massacre it's usually portrayed as. The civil war which followed Romanos' capture and eventual blinding is what ruined the empire and destroyed the themes, allowing the Turks access to Anatolia.
If I did add the tagmata, Byzantium would begin in 769 with the Scholae Palatinae (Scholai by now) and the Excubitors (Now known as the Exkoubitores), each 4,000 men strong. Two more tagmata, the Arithmos (Watch) and Hikanatoi (Able Ones) would be available in 867, each 4,000 men strong, giving a total of 16,000 mercenary troops, or 22,000 if you include the Varangian Guard (Which was also considered to be a tagmata unit). There's also the Noumeroi (Number, included the men who manned the Theodosian Walls) and the Optimatoi (Originally a guard unit, but later became an elite logistics unit), which were guarded Constantinople.
By 1066, the four main tagmata would rise to 6,000 men each (Something I can't portray in-game unless I made larger clones), and the Hetaireia would have become a major part of the army. There's not much information on the Hetaireia, but it's probable it was around 4,000-6,000 men strong. There's also the short lived tagmata of the 10th century emperors, such as the Immortals, but they are so minor that I can essentially ignore them. Anyway, in total, Byzantium would have access to 36,000 mercenary troops in 1066, 90% of which would disappear after 1078. Some of the tagmata continued into Alexius' time (The Varangians and Hetaireia), but they never fully recovered.
I could add a decision to allow Byzantine players to revive the tagmata after 1078 if they have the money, but this seems much too complicated for me. We are talking here about tens of thousands of troops, more if you want Rome to have legions. If I gave the Roman Empire ten legions of 5,000 men each, that's 50,000 men at your direct command. I honestly thing I'd rather use retinues to represent the tagmata and the legions. I added a legionary retinue for Roman culture characters, and the tagmata were all heavy cavalry (Expect for the Varangians, of course), which the cataphract retinue covers really well. I could rename the cataphracts to tagmata to make it more historical.
I would like to do something to boost retinue numbers for Rome and Byzantium at the expense of levy numbers. If I could do this, and find a way to make the Byzantine Emperors start with pre-formed cataphract/tagamta retinues, I could represent the tagmata much better. Mercenary units are difficult because you can't change the sizes and the cost necessitates you give a realm more money, which can lead to it becoming a superpower. The Byzantine Empire was certainly strong in the Middle Ages, but it wasn't the superpower it was before Islam. I've tried boosting retinue numbers through laws, but it doesn't seem to work. The administration laws would work well for this.