I personally believe that there was a mixture of fathery love as well as scientist fascination. Does it really have to be either or?
An earlier poster mentioned that Hojo would not have been a father if it weren't for this experiment. Well, he could have used any old fetus for this experiment. He chose his own because he might have thought that giving his child the powers of the ancients to be the best thing for it. There was no elaborate scheme of any kind at the beginning, because the guy honest to god did not know that Jenova was a parasitic monster alien. Proof? In crisis core, Hojo tells Zack that Genesis had been a memento from an "unenlightened era, when men could deem any unclassified life form an ancient."
Reasons why I think Hojo cared about Sephiroth: he helps him out and says that the only reason is because his son is in need of power and help. He mentions that Sephiroth looks down on him, so it obviously bothered him. He never mentioned how others looked down on him and hated him, only that Sephiroth did. Also, in before crisis, Hojo says that he has no intention of leaving Shinra just yet, because Shinra is the only place for Sephiroth. (Chapter 10) And in crisis core, he was supposedly the founder of the silver elite, the Sephiroth fan club. That club had personal things, frivolous things about Sephiroth that were unrelated to his value as a specimen. The club knew that Sephiroth was left handed, what he named his attack and weapon, what he washed his hair with, that he hung out with his friends in the soldier training room, exclusive photos, etc. and right when Zack escapes from Nibelheim five years later, another letter pops up from "chairwoman H" saying "sephiroth will never die! As long as I live so will he!" and other things about Sephiroth living on in their minds and having a plan of some kind. So, the Jenova reunion theory was just a plan to be reunited with his beloved son, AND to test it out. In Hojo's missions in CC, he mentions that things would have been far more interesting had he arrived at Nibelheim a bit sooner.
All in all, I think there was something but at the end of the day, it still doesn't change the fact that Sephiroth is still an intriguing specimen and Hojo is still a scientist. After all, did he ever aid Red and Aerith? No. Did he make clubs for them? No. Did Sephiroth get to have a life of some kind and did not even know that he was a specimen. The fan club was just evidence that Hojo paid attention to Sephiroth on matters outside of scientific observation. Why do that? Someone earlier mentioned that Hojo was trying to compete with Angeal and Genesises clubs to beat Hollander. But while it was implied that Hojo was behind Sephiroth's fanclub, it was not implied that Hollander was behind Angeal's. in fact, Hollander might have been even colder and less loving towards his son Angeal since he left Angeal in Banora as a child and he was raised by his mom and step dad (who gave him the buster sword). At least Hojo was there for Sephiroth, watching over him from a distance. But then again, Sephiroth was a greater success, had no mother, and Hojo also did sort of pay attention to Aerith's whereabouts, but it was mostly Shinra who wanted her because he wanted to find the promised land so he could create his Neo Midgar.
). Hojo could never love any other living creature because he was a textbook mad scientist, always seeing anything else as research lab material and Seph was no different.