I couldn't find this information anywhere the way I wanted it so I present to you:
List of Choice-based, Version, and Safari Exclusives
|002||Ivysaur||Friend Safari (E)|
|005||Charmeleon||Friend Safari (E)|
|008||Wartortle||Friend Safari (E)|
|037||Vulpix||Friend Safari (B)|
|038||Ninetales||Friend Safari (E)|
|090||Shellder||Version Y (B)|
|091||Cloyster||Version Y or Friend Safari (E)|
|120||Staryu||Version X (B)|
|121||Starmie||Version X (E)|
|127||Pinsir||Version X or Friend Safari|
|138||Omanyte||Version Y Helix Fossil|
|140||Kabuto||Version Y Dome Fossil|
|144||Articuno||both versions if you chose Chespin (L)|
|145||Zapdos||both versions if you chose Fennekin (L)|
|146||Moltres||both versions if you chose Froakie (L)|
|214||Heracross||Version Y or Friend Safari|
|246||Larvitar||Version Y (B)|
|247||Pupitar||Version Y or Friend Safari (E)|
|262||Mightyena||Version X or Friend Safari|
|304||Aron||Version X (B)|
|305||Lairon||Version X (E)|
|309||Electrike||Version Y (B)|
|310||Manectric||Friend Safari (E)|
|345||Lileep||Version X Root Fossil|
|347||Anorith||Version X Claw Fossil|
|510||Liepard||Version Y or Friend Safari|
|538||Throh||Version Y or Friend Safari|
|539||Sawk||Version X or Friend Safari|
|651||Quilladin||Friend Safari (E)|
|654||Braixen||Friend Safari (E)|
|657||Frogadier||Friend Safari (E)|
|682||Spritzee||Version Y or Friend Safari|
|684||Swirlix||Version X or Friend Safari|
|690||Skrelp||Version Y (B)|
|691||Dragalge||Version Y (E)|
|692||Clauncher||Version X (B)|
|693||Clawitzer||Version X (E)|
|696||Tyrunt||both versions if you chose Jaw Fossil|
|698||Amaura||both versions if you chose Sail Fossil|
|716||Xerneas||Version X (L)|
|717||Yveltal||Version Y (L)|
Info was compiled from lists found on serebii.net. Please feel free to let me know of any errors you come across and I'll look into them.
(L) means legendary so you can't breed them and there's one per game.
One Legendary Bird (144-146) is available to catch per game based on your first starter choice, so you have to trade for the others.
The new pair of fossils involve a choice so you can only get one per game, but you can breed and trade for the others. The other fossils are found postgame by using Rock Smash in the Glittering Cave.
(B) means you can breed something on the above list to obtain it, generally the entry below it.
(E) means you can evolve something on the above list to obtain it, generally the entry above it.
With the exception of the starters and fossils, this list only includes Pokemon you can catch in the wild. That's why 090-Shellder and 091-Cloyster are both on the list, 248-Tyranitar and 509-Purrloin aren't. This was done to cut down on list size since you can breed or evolve something else you've chosen or traded for and be able to get everything. This list doesn't include version exclusive mega stones.
I did this as a reference but feel free to use this thread to trade for these, unless you think an overall trading thread or google doc would be better suited I have one spot left on my friend code list I'm going to keep for trade purposes in someone isn't already on my friends list. Even with 99 friend safaris and over half of them having three Pokemon, I'm still having to trade to obtain a few that I can't catch on my own. I might look into doing another table for Pokemon that have to be traded to evolve and what conditions or items are needed to do so, because that goes along with the overall theme of needing outside help to fill out the Pokedex.
My goal is to see if I can complete as much of the Pokedex as possible before the Pokemon Bank is released at the end of December. I only have a copy of X, but I've managed to get almost all of the above checked off thanks to people in this forum and some GTS trading. For the Legendary exclusives, I caught the one available in my game, which was Articuno. I then traded it for Moltres, traded Moltres for Zapdos, and finally Zapdos for Yveltal. I have the birds on my GBA carts which I can import up eventually assuming I beat a gen 4 and 5 game at some point. Hope this is useful to someone.