I'm not trying to rewrite the rules or anything but I personally think with so many folks playing, I think Religions should be open providing they do not change your alignment. So Good civs could go with FoL, RoK, Order or Empyrean. Neutral Civs anything but Veil. Evil civs FoL, OO, Veil or Esus. With the Caveat that if you found it, you must be actively trying to spread it to your neighbors at all times, so if you've got open borders it's your responsibility to send a disciple to your neighbors, providing their alignment allows for your religion...that and if you found 1 you can't found a second. The more important question is what happens when you get 2 religions in your empire? Go with the flow and spread it some more, allow it but no further active spreading or send your Priests in to Inquisition the offending cities? I would suggest sticking with my original idea if it's a religion that would change you're alignment then you must cleanse it otherwise it's ok to keep, possibly spread it further but I'm not sure on that one. I suppose I say this as playing the Malakim, the supposedly most religious fanatical oriented civ in the game, and I'm left with no option to found a religion, it leaves me somewhat disappointed
For Wonders there is already a favorite wonder for every leader, I compiled that list of what wonders the various Leaders favor:
Valledia/Dain > Crown of Akharien
Keelyn > Syliven's Lyre
Perpentach > Theatre of Dreams
Sabathiel/Capria > Aquae Sucellus
Alexis/Faeryl > Soul Forge
Flauros > Pillar of Chains
Jonas/Sheelba > Dragon's Horde
Charadon/Mahala/Beeri/Decius > Form of the Titan
Ethne > Shrine of Sirona
Einion/Cardith/Arendel/Basium > Temple of Temporance
Grigori > Hall of Kings
Tasunke > Guild of Nine
Rohanna > Ride of the Nine Kings
Auric > Bone Palace
Hyborem > Infernal Grimoire
Arturus/Kandros/Garrim > Guild of Hammers
Falamar/Hannah > Great Lighthouse
Amelanchier/Varn > Tower of Eyes
Thessa > Catacomb Libralus
Tebryn/Os-Gabella > Prophecy of Ragnarok
Sandalphon > The Great Library
If one civ gets multiple's via different leader preferences then those remain the domain of that civ, so Balseraph's would get Theatre of Dreams & Syliven's providing there's only one Balseraph player, so I guess my exmple is a bad one, seeing as we've got 2 potential Balseraph's players

If multiple civs like it then it's a competition between those civs, so say you're Beeri you're competing against both Doviello's and Decius for Form of the Titan (this is an odd one though, Form should be excluded from Civ's defaulting into the competition via multiple leaders for this one). Whatever is left can be assigned or open to all, depending on the nature of the wonder.
These are just my thoughts on it though, I'll go with the flow. Although I do think keeping religions open based on alignments is the way to go, if you get beat to it it's not to big a deal with the free disciple, you lose out on the holy city but it creates conflict, aside from simple good vs evil.