I have no fond memory of Battle Isle but I really loved FG.
You kept your army from one battle to another, each unit could evolve with experience. The campaign had you progress through a map where you could choose a path or another with enemy armies adapted to the terrain you were crossing (desert, plain, mountain, more cavalry, more infantry or aerial units etc..).
Losing an unit you had since numerous battles was quite heartbreaking. The difficulty was quite steep? Or maybe it is just my memory of it?
After several battles your army was really yours because of the choices you had made for the recruitment and the evolution of those units.
In BI all this was quite impersonal and as you said like a puzzle game.