Ayenew, missteps in theology are different than other kinds of things, no? It can be argued whether or not he handled personally any particular matter in the right way, or if it is a good thing or not to have so many general bishops, or anything like that. But if you read, for instance, of his conflict with Fr. Matthew the Poor over the issue of Theosis, it is clear that Fr. Matthew understood it, whereas HH did not. Or, rather, what HH was responding to under the banner of 'Theosis' was not how that term is actually defined. That is why I wrote that either HH did not understand properly, or he was just not able to articulate his objections properly. I would prefer to believe as his defenders in this area have pointed out (and I have been one of those, in other contexts than this thread), that HH was responding to bad Arabic translations of the concept that made it sound like we "eat" the divinity (as in, it is consumed by us in the Eucharist the same way that regular food is), but that doesn't make the critique any more correct with regard to Fr. Matthew's understanding (which was not the same as those bad translations). Thanks be to God, both men were reconciled to one another before Fr. Matthew's departure.
There are proper OO objections to the EO understanding of Theosis (though this would not be the place to get into them, and they are more technical, in the sense that the priest in question feels that a different, related term fits our theology better, and hence we ought to not "piggy-back" on EO theological terms we may not even understand, lest we give our own people the wrong idea of what we believe), but neither EO nor OO believe that we "eat" (consume) the divinity, so any critique that is based on that is out of line with what any church actually affirms.
HH Pope Shenouda III is probably my favorite recent Pope, too (again, I'm too young to have known any other). I do not think it is necessary or even particularly wise to affirm absolutely everything any given leader may have written or said, as though he is immune from making mistakes or not completely understanding everything. Since we do not believe that our Pope is infallible, it shouldn't be impossible to say "Yes, I think he erred in this particular instance", and yet still hold him up as a good model, or a good teacher in other aspects, a saint, etc. Consider how the very same people who have alleged that he was heretical for "rejecting Theosis" (even though, again, what HH was rejecting was not Theosis, whether he himself understood that or not) have also recently published new editions of some of his writings (Eastern Orthodox publisher St. Vladimir's Seminary Press republished his work The Life of Repentance and Purity in 2016).
I believe, of course, that HH was and is fully Orthodox, but we shouldn't kid ourselves into thinking that he was an academic theologian. He wrote much, but his specialties were definitely more in poetry and ascetical writings and the everyday application of the faith than in some kind of exhaustive, systematic theology. We need both approaches (and we certainly have both in our Church), but when I want something more comprehensive I will turn to our more scholarly writers like Fr. Shenouda Maher Ishak, Fr. Tadros Y. Malaty (especially his "______ in the Orthodox Concept" series; his writings vary greatly in their level, as he has also written introductory works and compiled commentaries from the fathers), Fr. Athanasius Iskander, Aziz S. Atiya, Maged S.A. Mikhail, etc. People like HH Pope Shenouda III, Fr. Matta El Miskeen, and others are more like the ancient fathers like Mor Philoxenos of Mabbug or similar: practical theologians, who came from the desert and were best suited to it and understood in that context. After reading more of HH's biography in various places, watching old interviews with him, and reading his poetry, part of me thinks that he probably never really wanted to come back from exile in the desert, but knew he had to in order to shepherd the Church. That in itself makes him commendable to me. May God accept his intercessions for us, his children.