Which Civilization/Nation should I go for? Assuming it is around SS1-SS7 of MLP being invaded first, yet, Equestria has some advantages in the early parts. Here are some rivals I got in my mind:

1.) Reign of Sozin-to-Ozai's Fire Nation

Advantages

• No Sozin's Comet in Equestria.
• Princess Celestia & Princess Luna can causes Solar Eclipse for periods of time, blocking firebender during that.
• Most Ponies are physical stronger than average Fire Nation's Infantries.

Disadvantages

• (After Fall of Ba Sing Se) Dai Li are also on Azula's side, as both firebenders & Dai Li work together. Plus, they are not affected by solar Eclipse.
• More Advanced Military Technology of Fire Nation, especially on tanks, metallic airships and drills.
• Azula might offer cooperations with local creatures who are rivals to Equestria, yet, may betray some & become the leader.

2.)Thrall Clan-turned-Warlord Skaven Clan (Skrye/Moulder)

Advantages

• The Skaven Clan is considered weak & small in number in the early part, before they have been settled firmly somewhere & have their schemes & knowledge upon Equestria well.
• There is no Warpstone, their main energy sources, in Equestria.(But, they may find alternate(s), later)
• They are fragile to ponies' strength, when it comes to 1v1.

Disadvantages

• After they have spreaded their Under-Cities & corruptions, they will become the threats difficult to get rid of.
• They can create both mutated warbeasts & deadly magitech engines after they figured out how to in the new world.
• They reproduce quickly, and difficult to be catch. Their strength is in cunning, stealth, agility, and number.

3.)Genestealer Cults

Advantages

• Smaller in numbers, as the early generations of Hybrid are considerably noticeable.
• Relying on smaller-scaled guerilla warfare raiding on the early phases.
• Low reproductive rates in the early generations, may relies on infections & propagandas.

Disadvantages

• After some Generations, they hybrids become more resemble to locals enough to infiltrate into governments & authorities, yet. loyal to the cults.
• The cultists are absolutely loyal to their causes, and can corrupt others as well. By both propagandas, cult-invitation, kidnapping. etc.
• Difficult to be discovered their cult somehow. Most the discovering ones are 'taken care of' before the news told.

The intruders are teleported to Equestria, not in full number, but enough to have fair chance to survive & occupied few of small towns. They may recruit the member among their kinds in limited number by 'magical method'. Equestria would heard about them as rumor first, until the serious damages happened somewhere.