@Background Pony #C262 
True, there’s always a risk of making a critical mistake and losing when fighting a much weaker opponent because you went from being confident but methodical to getting cocky and half-assing it. There is a difference between playing to the strengths of your own forces while exploiting the weaknesses of the enemy, and being suicidally aggressive by just throwing wave after wave against the enemy and needlessly turning it into a war of attrition (or worse, lured into a huge trap). I guess it would be easier for me to come up with a strategy for the CIS if I knew what their whole objective is with conquering Equestria. I just went with the harvesting resources angle because I simply couldn’t think of any other good reason for the CIS to invade Equestria in the first place. Keep in mind the only context I have for this conflict is this picture, I have no idea if there’s supposed to be an actual story behind this or not. To me it seems like this war would be a relatively easy, but ultimately pointless, victory for the CIS.

@Genetic_Beast_Lobster 
That’s more of a plan if they want to harvest a mineral resource from the surface. But they better not try to get too overconfident or Klendathu mess could happen. But if they want the living resources from there (the federation is just a cover to build the Empire later), that tactic might not be the best. It would be like capturing a city that has burned down to the basement.

@leondmaster  
They could definitely do that, but I don’t think they would even need to go to that much effort, especially if all they’re concerned about is harvesting whatever valuable resources are there. All the Confederates would really have to do is bombard the living hell out of every major population center and military facility from orbit and only send in ground troops to mop up whatever is left, it’s not like anyone planet-side could do anything about it. Oh no, the ground forces are encountering heavier resistance than anticipated? Not a problem, bring them back into orbit and start the bombardment again, rinse and repeat until the enemy either gives up or gets wiped out.

@Background Pony #5208  
Having magic might help, but the confederate military is massive and in the star wars EU they gave the republic a run for their money. Ultimately we are talking about an invasion of aliens with superior technology, numbers, firepower, and resources. Seeing as equestria doesn’t have space ships of any description they can only wage a defensive war that they can never truly win because the confederates can just setup a droid factory and some mining facilities in the equestrian star system without fear of counter-attack. Then endlessly pump out new droids until the enemy is overwhelmed by sheer numbers and forced into peace talks.

@Background Pony #4B8E  
Well, attacking first such royal guard will for sure wipe them out. But as you say, they are utterly incompetent anyway. They don’t have guns, where they can have magic arrows and disintegration spells. No fallout shelters required if the enemy doesn’t use nuclear weapons in the first place. The economy of Equestria is clearly not based on desserts.  
And there is a proper wartime leader, the four alicorns. Just that in S5 finale no rainboom means no effective leader against Sombra. In this case, all of the alicorns can gather in the Crystal Empire, Twilight get the powers as a one-mare army in the frontline and the other three, more experienced, guide the rest of the ponies against the invaders. After they know their enemies, they can launch much more effective attacks against them.  
Oh, and their allies will surely help against an alien menace that threatens the entire world, unlike King Sombra.

@Background Pony #5208  
equestria basically the USA, except without the gun nuts, conspiracy theorists that crowdfunded fallout shelters, and a royal guard whose eptitude begins and ends at armor polishing, no national guard of freetime soldiers either if memory serves.  
an economy consisting of pie and pastries.  
and replaced by whom exactly, as mentioned there ARE no proper wartime leaders.

@Background Pony #4B8E  
Equestria is basically the USA. Remove the principate leadership and main corporations directives and new ones will rise very soon. And without the element of surprise anymore, all of the Equestrian economy will be put into the war effort to defeat some invaders who doesn’t even have magic.  
They will strike the leadership, leaders very competent on peace time, but who would have been replaced anyway during war.

@Background Pony #5208  
decapitation strike, leadership, weather control, main defense power.  
the general knows exactly what he’s doing.

Attack the most well defended centers of military and political power first?  
The General doesn’t really know about tactics.