There are two aspects of MM which irk me. Two that I can remember, anyway; there may be more that I have forgotten. I will list this deleterious duet here, as I enjoy complaining about things.
The first issue I take with MM concerns the Worst Turks. The Ottoman state is unfairly afforded continuous free casus bellis on the Knights of Rhodes after a certain date. This is only the beginning of my troubles concerning the Ottomans, but let me elaborate on it in order to demonstrate it's troubling implications and relations to other ill aspects of the Ottoman's in this mod. The endless, free casus bellis mean that playing as the knights of Rhodes one will find himself in an interminable series of wars with the Ottomans for the latter half of the game. Even if you manage to beat and cripple them, their handicaps are such that they can easily and inexorably recover.
The only hypothetical scenario in which the Knights could avoid this perpetual war would be one in which the Ottoman Empire is utterly destroyed. Playing as the Knights this can only be achieved by usurping every last one of their regions yourself; no other means can work. One cannot rely on the AI to do it for him, as there is no AI state that can challenge the Turk. One cannot hope to reduce the Ottoman Empire into constituent states through peace treaties, thereby castrating it's power -- that is impossible, because the Ottoman Empire will simply peacefully annex any states split off from it, as most of the states constituting Turkey proper have a pathological tendency to request annexations, no matter the circumstances (I believe this AI tendency is hard coded, or else achieved through an event). One cannot hope to mire the Turks so deeply in debt, wars, negative stability and inflation that they could not ever hope to recover, as some combination of their innate abilities and MM features in general allows themselves to swiftly recover from seemingly hopeless situations. So, unfortunately, playing as the Knights means that one will have to suffer the burden of conquest, either of the Turk over oneself, or oneself over the Turk, as there is no other outcome that they can hope to achieve. Not only that, but playing as any state bordering the Turk means almost the same thing -- the only difference is that war isn't designed to be certainty -- the ability of any state to reduce the Turks permanently relies on the state's ability to personally conquer and hold (or else dole out to it's allies) all of Turkey's regions. This is troubling, as it not only makes the game a pain to play, but it makes divergence from Ottoman supremacy a near impossibility.
The second issue I am concerned with is the piracy shebang. This issue is quite a bit simpler, so much so that I can demonstrate it in it's entirety in only a few sentences. Quite simply, every coastal region one owns increases the provincial risks of piracy for all of his other provinces incrementally at a rate that cannot be offset after a certain point. Should one continue to add coastal provinces to his Empire, he would at some point find every one of his coastal regions in a state of rampant piracy, regardless of any countermeasures he could possibly take. This oversight (I can only assume it's one, there's certainly no historical or balance related explanation for it) drastically weakens coastal empires and makes them a pain to play.
So, there you have it. Two flaws in MM. I will admit that I enjoy the mod in spite of it's shortcomings, but I can only see it's shortcomings as being the unnecessary results of poor design and stubbornness on the part of it's creators. The team responsible for it obviously had a lot of room for improvement, and it's easy to see why their later project was such a catastrophe. So, hurr hurr, Ubik sucks.