Ok, finally caught up with negima and this manga...
Well, as a few thoughts:
By now we know negi is pretty much alive but like his father before him missing. The issue is why and it probably has to do with fate's recent comments. We saw negi in nagumo's flashback and that was only 20 years ago. Not to mention that negi seemed to still be young and he was called the most immortal or something. Perhaps more interesting is the fact that negi's magia erebea had changed a decent bit from his youth which seem rather weird. He had the wing things touta has and to boot his actual body seemed more demonic. I guess a lot must have happened since then. Maybe the magia erebea we saw back in the day was not even properly developed. We even saw negi did not appear to have that a strong regenerative power. I wonder if he ever did surpass evangeline...
Anyways, as for fate I don't think the issue is that he is evil per say. To me it kinda seems like he is very utilitarian and a numbers person so to speak. I guess he could have changed in the past 80 years or so but to me it would be unlikely. Seeing his attitude towards touta it would seem like touta has something that fate specifically wants for whatever reason. It would be weird if it was touta himself considering he did not hesitate to tear him apart and seemingly take him. I guess his immortality might deal with that although it is also entirely plausible that touta being alive is not quite important here. As for what touta could have... If we assume any consistency with his old character it would perhaps make sense that touta has something that can be relevant to the elevator, mars and such things. Touta seems to have quite the lineage so far (related to negi, strong possibility of asuna, and somehow to konoka apparently even though she was a lesbian) so maybe he has some other remarkable magics even beyond magia erebea. If he got healing powers or his own magic nullification then perhaps that would be pretty important, it could easily relate to some plot points from negima. Then again fate was called the most evil dark mage however that might as well be an issue of perspective. Plenty of other characters have had murky roles in history so far (nagi, eva...).
My take is also that the enemy will be the mage of the beginning. It kinda seemed like negima did not really quite deal with him appropriately and was left for this sequel. Even in the end a lot of the plot points were dealt with by the old folk and eva rather than negi and his harem.
One thing I do find a tad weird is that touta has magia erebea at all. Should he have that? His situation is quite unlike that of his grandfather... Negi got it from training and then the thing made him immortal. In turn touta got it seemingly straight from eva. Does that make sense? Is it something innate of those with eva's brand of immortality? What seems weird is that magia erebia is supposed to feed on the darkness of the user. Negi had an affinity towards that from the start which is why he was able to learn it and eventually overcome it. But he did it embracing the darkness and that stuff. In turn touta is a polar opposite to negi, he seems to be more like nagi (and asuna). Negi was calculating, he did not have that "idiocy" factor which rakan or his dad had and the two of them were from the light so to speak. Touta is precisely the kind of idiot they were, a far more straightforward shonen hero. Well, touta does not like to fight and he does not even seem to properly enjoy being so adept at fighting but that only makes the situation weirder. So that he has magea erebea and that he is able to overcome it seems kinda cheap here. On the other hand the case can be made that there is some huge darkness to touta which is what allowed him to use magia erebea and overcome it. Perhaps that even relates to what fate wants.... It is also interesting to note just how much unlike negi touta is. Along with his personality it seems like touta will fight completely unlike negi. So far it would seem like touta will be more like nagi... A few spells and then just kick ass the old fashion way. Maybe kanka? Kanka and magea erebea would be too hax though. There has to be more to his style in the future anyways, I doubt he could survive as an immortal if he limits his fighting to fighting like a mortal. Then again ki alone seems to be able to come a long way.