I disagree about different systems making little impact beyond graphical and user interface. I think it can make drastic differences in gameplay and game design, particularly in the logic that drives them. I'm struggling to organize all my thoughts around it without some graphical representation, I will do some mockups to continue the conversation.
I like the way you are thinking here with the fire and lightening examples. Gameplay diversity is key, with cost and benefits related to various choices that can also alter situationally. However, I do believe that various Grid Systems
to have a significant impact on what can be done, how it is done, and the logic behind it. For example: What I'm currently intrigued about in regards to the Equilateral Triangle system is how the six connections to each vertex can relate to team attacks or synergy between multiple characters. Such as in this image:
Now this system can and has been done with a grid system (Joan of Arc), but it is more flexible and intuitive with the triangle system.
Regarding baseball and throwing spears. I like your ideas, but I'm struggling to fit them into a traditional SRPG format. Turn order is just so crucial with single character turns at a time and no real time combat. Valkyria Chronicles is close to what you are talking about, and Frozen Synapse is kind of closer but also much farther away. Both games and strategically very cool and different than FFT. I guess what you are looking for is more AI driven passive/reactive skills for your units.