1. My reference ruleset for magic is RMSS/FRP. I use Spell Law, plus Mentalism/Essence/Channeling/Treasure Co in free access. I don't use Arcane Companion. I control access to Elemental Co, as well as to all the companions of the RM2 line and the RMU beta Spell Law and Treasure Law. In this campaign, I have used one list from RMU beta Spell Law, one list from RM2 RoCo1, one list from RM2 AlchemyCo, one list from RM2 RoCo5, one list from RMFRP ElemCo, and the others from the RMSS/FRP Spell Law and magic Companions. I have two Semi Users, one Hybrid user, and one Pure User.
2. The players choose the list, subject to GM comment and ultimate veto if I really don't agree with something. They usually tell me what kind of character they want to play, then we agree on a professsion, and then they choose the spell lists and I review their picks.
3. Base Lists are only indicative. If someone wants to take lists from other professions or other companions as base lists because it fits their concept better, they can, within the limits of point 2 above. Basically, players can assemble any set of base lists as long as it makes sense to them and to me and I don't find it overpowered.
I also took a leaf from RMU and made developing Open Lists the same cost as Base Lists. On the other hand, Closed Lists cost significantly more, which means that if people really want to develop some Closed Lists, they take them as Base (otherwise, the DP drain becomes painful).
They can only develop 2 ranks per list per level (cost is typically x/y, except for non spell users for which it is simply x). On the other hand, they can develop as many lists as they want in a single development, provided they have the DPs, of course. Since y is typically equal to 2x, there is an incentive to develop width-first instead of depth-first.
Spell Lists development costs are reduced for Semi Users, and significantly reduced for Non Users.
All spell-casting requires one roll only: the list skill bonus is used to cast the spell, except for directed attacks where the appropriate DS skill bonus is used instead. For non-directed attacks, target RR comes as a modifier to casting roll.
Since I use player-facing rolls, if a NPC casts a spell on a PC, the NPC does not roll for spell casting. Instead, the PC rolls resistance (same idea for directed spells : the PC rolls defence).