Skill links and skill chains?

For both of my current projects, both the huge long term one and the RTP based stuff I want to add a bit of extra functionality to the battle system. What I am looking for is explained below and perhaps some of my ideas. I would appreciate any advice on how to implement these.

For the big project this is in the vein of skill/assist links, like they are in the Front Mission series of TRPGs. The big project is a TRPG as well (once I finish making the battle system, haven't had much time in the past year to even touch RPG maker due to college). What I want here, for those who havent played the front mission games, is a system iun which there are passive skills and even active skills that can go off if a nearby ally is attacked. In game you would be able to set your own links via menu. What I am wondering is if this style of combat system augmentation possible via a set of conditional branches that just check if these links are set and if the skill can be used at their current range. If it can, gives the option to use the ability at the cost of that characters movement/attacks for that round.

As for the one for my RTP project, I am pretty sure this functionality is possible but would likely involve much in the array and matrix use. There would be a command introduced later on known as "COMBO", basically the idea is a character would build up skill charges over the course of a battle (each battle would start at 0, unless there is a surprise attack or such.). Basically when combo is used, characters can input a series of skills which would combine into a new, special skill that would be used for that round. Would the matrix/array and branch to skill approach be effective?