Its very odd to me that as the timelines were getting worse according to Twilight, and Flim and Flam were just before the Wasteland timeline.

Not only is this suggesting that they would have been a threat to equestria, but that they would mess up the world more so than either Nightmare Moon, Tirek, Discord, Sombra or Chrysalis. They are only rivaled by the wastes.

Is there more to them than what meets the eye?

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I would think Ahuizotl or even the Diamond Dogs could become bigger threats. One is a power-hungry creature with no moral qualms, and there seems to be a large empire of Diamond Dogs:

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I don't think they were the cause, but maybe a side effect.

I think Twilight "Celestia'll send me back to magic kindergarten!" Sparkle is just prone to hyperbole.

Consider the implications of each timeline:

Sombra returns: A land ravaged by ongoing war. Ponies unite, fight, and live on.

Chrysalis wins: A land ravaged by a lost war. Ponies hide and resist, but are losing.

Nightmare Moon wins: A nation ruled by a tyrannical overlord. The sun never rises. Ponies live, but are complicit in their subservience.

Tirek rampages: A land torn apart by a magic eating brute. Survival is not guaranteed, but perhaps you can live if you relinquish your magic.

Discord reigns: A land where the laws of physics no longer apply. Suffering abounds. Ponies are at the mercy of a mad god.

Flim/Flam corporate takeover: A land where progress and money are the highest priority. Note the pollution and mass deforestation. Perhaps a prelude to a world ravaged by global warming? Precursor to Bioshock? Note that this is the only timeline where it is explicitly revealed that regular ponies did it to themselves.

The Wasteland: Fallout Equestria now canon.

I think that's a pretty good downhill slope.

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Sombra- External Evil, wants to rule, Crystal Slaves
NMM - External Evil, wants to rule. Eternal Night
Chrysalis - External Evil, wants to rule, noms
Tirek - External Evil, wants to rule, hold all the power
FF Bros- Internal Evil, want to rule through corporate domination / destruction of environment

4886480 I still never liked the fact that some comics and now this future seems to set them up as true villains, instead of just shady salesmen and con-men.

4886480 It does seem like it's local to what was Sweet Apple Acres. One can argue that they spread their business over Equestria and I don't know, pollution? Kindia reminds me of Dr. Susses': The Lorax. But in Sombra's is in full industrial mobilization. Maybe she's exaggerating but if all else is true, the order of severity is as followed:

Flim Flam.
Discord. (It's Wonderland, looks fun to me)
Nightmare Moon. (No one is complaining after all)
King Sombra. (Ponies not under Sombra seems to manage outside of battle)
Queen Chrysalis. (We don't know what changeling rule entails. Sure the ponies must feed them, but how do they feed and what are the effects? Is it passively absorbing love essence or the whole cocoon thing as in many fics? Will ponies be fine or is it like Shining Armor under Chrysalis' spell? Are the resistance ponies afraid of changelings just because they feed off ponies and took over Equestria or is there more? We'll just assume the worst.)
Lord Tirek. (It's pretty much the apocalypse)
Wasteland. (It is the apocalypse (post-apocalypse to be precise))