Well, it has been a while since I've played vanilla FfH, and I actually skipped .23 (I was stuck with dial-up over the summer, and .25 came out just before I moved back to college), but I'll help if I can.
Not sure why you can't adopt a religion. What religion are you trying to adopt? No one can adopt Cult of the Dragon, but of course the elves can't found it either so I doubt that is relevant. In BtS FfH an AI weight of -100 prohibits even human players from adopting it. That might be the case in .23 too, but I I just looked at the xml and she doesn't have such a weihghting to any religion but CotD. Are you sure you really founded the religion? If you were not the first to research a religion founding tech you would get a disciple unit instead of a holy city, so you would have to manually spread it before you convert.
The only other thing I can think of is that you must wait a minimum number of turns between converting. You hadn't just adopted something else a few turn earlier, did you?
BtS is definitely better. Of course, there are a few things that Kael decided not to include in the BtS version that I wish he had, but he was concerned about bugs and performance issues.
Hidden never got implemented. Kael said it would have something to do with espionage, making known maps degrade, or something like that, but he changed his mind about it. It has been implied that these would eventually be related to the Council of Esus religion and/or passive effects of shadow mana, but those particular ideas are not in the game. I do think that it it reduced the cost of Thieves Guilds though, but that isn't much compared to the other traits. In Shadow, Faeryl has Arcane/Raiders and Sandalphon (Morgoth was renamed, sine most people though "Dark Lord" when they saw this neutral leader's name) has Industrious/Defender.