OK so off the top of my head a quick breakdown of the big differences:
1) No prophet - nobody in the game can declare Prophets
2) Scales, Dominion strength, Bless, and Awake/Imprisoned/Dormant are determined by the Pretender build. Disciples awaken in half the time of the Pretender (+- a bit for RNG). Disciples get Bless and HP/stat buffs/debuffs according to dominion and cannot be bless outside of their dominion, just like Pretenders. If a Disciple dies, it can be prayed back to life by priests, and allied priests should be able to aid in calling for the return of an allied Pretender/Disciple
3) The amount of Temples required to increase your Dominion by 1 is equal to 5 * # people on the team and are counted as a team. So since we have teams of 2, your team requires a total of 10 temples for +1 Dom
4) Despite not being priests, Disciples can claim Thrones and have 1 Temple Check per turn (Pretenders still have 3 checks with 1 guaranteed)
5) Team shares the dominion effects of the pretender. Any dominion effects of disciples will not take place, BUT their bonuses like cheaper/more expensive temples, labs, and non-Dominion based special spawns/rules st remain. So for instance, if EA Arcoscephale is the pretender, all members of the team have Scrying in dominion, but if MA C'Tis is the disciple, then the dominion will not spread disease. Freespawns seem to be different for different nations - EA Yomi still gets freespawn from temples, for instance
6) Teammates cannot view exact numbers, formation, combat unit stats, PD amount, or items of their allies provinces/armies/commanders in the game. Communication is key!
7) Teammates WILL receive every battle with their allies as participants, but ARE NOT guaranteed to see battles viewed by allied scouts - i.e. if your ally is attacked you will 100% of the time see the battle report, but if 2 enemy players fight and your ally has a scout in the province, you are not guaranteed to see the battle even if your ally does. Communication is key!
8) Allies will not receive details of your events, site searches, assassinations, messages received, or special commander actions each turn, although they CAN still pull up all events on any province owned by allies with the in-game province event log
9) Teammates can move freely within each other's owned provinces, HOWEVER, if attacked, only 1 army can be on the field, so you will not be fighting with your ally army or PD. If attacked with multiple armies in location, the owner of the province will always fight first.
10) If both allies attack the same indy province or enemy province, just as with normal rules, the RNG determines who got there first and orders battles accordingly
11) Forts do not pull resources from allied provinces
12) If both players have a commander in a province, the owner of the province will have an action available to cede ownership of the province to their ally, that takes effect the next turn.
13) You CAN site search or claim Thrones in ally provinces, although your ally will not receive notification of discovered sites, they will show up
14) Thrones are 'owned' by the Pretender of each faction, and apply full bless/scales to their entire team's Dominion
I think that about covers the major stuff.