@Fwelin  
Twilight’s freezing spell, again, is taking several seconds to cast and areal, so it can work against Dash only in confined space, otherwise she’ll avoid it easily. There’s a reason why Twi used it only on the targets who completely ignored her presence and not actively evaded or counter-attacked. Telikinesis spell, as I said, was shown to being able to holding filly or slowing down the grown-up pony. The only times when grown-up pony was actually being held down by it is when said pony either not actively resisted (as in “Daring Don’t” or “Lesson Zero”) or actually cooperated with caster (“Green isn’t your color”). Otherwise grown-up pony just rips through it (again the reason why Twilight is not using it in actual combat that much).  
It takes actually the whole damned army of changelings to capture the Mane Six, not just a score of them. Even the greatest heroes can be defeated if they outnumbered so vastly (and can’t even be sure who’s their friend and who’s foe in disguise). especially since Rainbow can’t use her strongest attack in a crowded city where the chance of… collateral damage is too high.  
In Sombra War timeline said war lasted for 2-3 years top (that’s how much time presumably passed since Season 3 beginning to Season 5 end which is time Twi returned to). Not so extended period of time in my book. Also, this timeline’s Dash can’t just Rainnuke Sombra forces because her not doing Sonic Rainboom (and therefore having no reason to try to recreate it) is the main diverging point between the timelines shown! Still, she managed to became Wonderbolt much earlier, than in the main timeline, and seems to be doing pretty well, so… given some time she’ll probably deal with Sombra threat just fine!  
So, I’m still convinced she’d be pretty effective in a fight with Zygon queen, especially with Twi providing the fire support!

@ShimmeringStallion  
God, Dammit, I realized I should’ve said “Ca-neigh-dian Tire”.

She’s clearly connected to a Portable Battery, available at Canadian Tire! =D

@Vaidelot  
Yeah, only because Twilight was not using any magic on her at all until the memory spell. In Lesson Zero, Equestria Games, and Castle Mania, she had zero problems immobilizing Rainbow on her own. Also, you know that 28 Pranks Later was not a battle, right?
 
Again, the Rain-nuke is a gag scene that Rainbow can’t actually do in serious contexts, similar to Pinkie’s offscreen teleportation, or Twilight getting zero injuries from a piano falling on her head.
 
Applejack can only do it when Rainbow Dash is nearby and only starting to accelerate; Twilight has done it while Rainbow was already moving very fast, and Starlight has shown the ability to land linear spells on Rainbow when she’s moving incredibly fast (when she zapped filly Rainbow when she was an instant from doing the Sonic Rainboom). Finally, Twilight’s freeze spell is essentially instant and can affect a huge range (it engulfed both mountains in The Hooffields and Mccolts), and it doesn’t strain her at all unless she’s holding several dozen ponies at once. Range doesn’t affect the difficulty, only the number of targets, and Rainbow is only a single pony, meaning Twilight would have zero trouble holding her (like she already did).
 
Rainbow was being held by two changelings because she was the only one being carried through the air, not because she’s more of a threat than any of the others. If she’s as strong as you’re claiming, ten changelings wouldn’t have been enough.
 
We saw that the war had been going on for an extended period of time and that King Sombra had taken over half of Equestria despite Rainbow’s participation (as well as the participation of other pegasi that are almost as fast as her, like Spitfire). If she could actually do stuff like the Rain-nuke, the enemy forces would have zero chance, and if she could successfully attack Sombra like you’re saying she could with the fake Twilight in this story, she would have instead of just doing hand to hand combat against normal soldiers (and have to get saved from a giant boulder).
 
Rainbow is incredibly fast and quite strong when compared to 99.9% of ponies, but she’s no match for the actual strongest, and she can’t do things like Rain-nukes outside of gag scenes.

@Fwelin  
“Isn’t closely as strong as Twilight” you said? Ha! Out of three confrontations with Dash (RoH p2, MMDW, 28PL) in two of them last of the Mane Six had to join their forces to put her down. And in the later case it takes coordinated efforts of the whole Ponyville to get even with her! And, speaking of Twi, the only time she managed to pull something as devastating as Rainnuke is when she wielded the power of the four Alicorns combined!  
Twilight indeed used telekinesis to hold Dash’s tail in LZ (and some other instances), but it was more akin to AJ’s using teeth to pull her tail and barely can contain a grown (and actively resisting) pony for long (Starlight did it, but to the unsuspecting filly). Speaking of the other holding spells, the one that Twi used in Castle-mania takes time to cast and clearly affects defined area (the bigger the harder it’s to hold). And Starlight’s crystallizing spell required target to be directly hit by it. Therefore, both of them are pretty useless against a fast and agile target.  
In ACW changelings actually managed to capture all of the Mane Six by sheer numerical superiority. And Dash was the only one that, even after being defeated, had to be personally held by two drones! And we’ve seen to few of said bad future to know, whether Dash turned the tide of the war or not.  
In short, Dash is the damned Überpony and not using her superior skills in battle here seems like a HUGE tactical mistake to me.

@Vaidelot  
Rainbow isn’t even close to as strong as current Twilight, let alone this much stronger future Twilight, and you’re way overestimating a joke scene (the Sonic Rain-nuke). Twilight has easily caught Rainbow in mid-air multiple times with her magic, including at very high speed, and Starlight even managed to land a laser on filly Rainbow when she was less than a second from doing a Sonic Rainboom. She’s fast and strong, but not that fast and strong; if she was as strong as you claim she is, normal changelings would never have captured her in ACW, and she would have turned the tide of the war by herself in the bad Sombra future.
 
If Rainbow tries to attack, she’s going to either get swatted out of the sky or grabbed and used as a hostage.

@Meanlucario  
Shield or spell powerful enough to stop pony approaching on a speed of sound? Doubt the queen could make one fast enough, and even if she could, she would be distracted long enough for Twi to strike. Dash is the most powerful of the Mane Six, so, even if the creature can hold her or Twilight alone, against both of them it would have no chance.

@Vaidelot  
You overestimate Dash’s abilities, and underestimate a creature strong enough to capture Twilight. A simple shield or levitation spell to hold Dash would stop her, and give her a prisoner/meat-shield to use against Twi.

@Meanlucario  
She won’t have the time nor the power to do so. Not only Dash is MUCH faster than anypony else, she’s also exceptionally sturdy (as her multiple consequence-less collides with trees/houses/other solid objects demonstrate on the regular basis), so, even if Zygon queen had time to react, her strike just wouldn’t be both fast and devastating enough to prevent Dash from finishing the Rainnuke. And when it’s finished… even if it’s not destroys her outright (which is doubtful), it will surely damage and disorient her enough for Twilight to muster a finishing blow.

And it looks like the dead Alicorn sister is not so dead after all. :)

@Vaidelot  
What’s stopping her from stopping her with magic and breaking her neck?

Just ask Dash to rainnuke her! It’s that simple!