At end-game, AI war had you manage a dozen different "fleet" ship types, a dozen "starship" types, each with randomized upgrade trees, potentially among 40 level high ?
I'd suggest something like M.A.X. did. In short, they had 2 researches "trees", one with "gold", the other with research (that point is completely irrelevant to AI war). What was relevant though, was that the research upgrades gave a bonus to ALL of your units / structures, like +10% hull to litterally everything. Second, "gold" upgrades were given to individual units / structures, and cost far less. Of course, the cost rose exponentially for each upgrade taken, ensuring that you had to use both systems.
In AI war the same system could be used, either pay for single units for upgrade or pay for an higher cost empire wide bonus... that would apply for everything.
The exponential costs would have to be balanced to ensure that no units are completely left behind, or possibly, you'd have to take an empire wide bonus for 5 "single unit" bonus (and buy them as packs).
I thought of them because they also used marks and roman numerals =). And, it went up very, very far.
One thing is sure though, I'd keep the name of levels "mark" and make it visible on the units, even if it goes to XV. And, keep roman numerals. Under C, everyone should be able to read them. But maybe an option to switch to regular numbers could be cool.