I made an account just to give this five stars
Loved it, rock on!
Ah, like the third time I've completed this game. And still fun.
The medals are buggy though, I can't get the Impossible! one.
And what do those guard towers do in the iPad version? No amount of Googling can tell me.
1+2: Minigames would be too hard to implement (you can't improve on scouting, and speeding up building/training/research would have way too much effect on the game.) Even if it's just the "shooting" minigame, this would be really hard to balance; if it (easily) gets a better result than not doing it, you'd want to manually do ALL the missions, so you could limit it to 1 mission/day manually.
Either way, it still encourages doing missions manually. If you want to shoot stuff go play the Last Stand, this is a strategy game. The only way fighting is a possible suggestion is the way Nick8akon already suggested, TBS combat.
3: Yes. It's called chance. ((How do you even get a 1% chance of success on a mission. And why did you try that? So I'll adjust your numbers to 90% and 10%)) A 90% chance is NOT a 100% chance, nor is a 10% chance the same as a 0% chance. And if you're getting really pissed off, there is still an autosave so you can save scumm. (Onoes, I lost a square to the attack! /load, put another gaurd on duty)
I've captured the whole city now what do i do ?