First of all, I am literally in love with this theory. I always didnt like luna for some reason....i always thought there was something up with her. and as much as people say "nah", you can't DISPROVE it with current canon and semi-canon (comics). It has a large amount of undenyable circumstantial evidence, which is not conclusive, but is not dissmisable either.
I just read the comic arc about queen chysralis (however you freaking spell it)...and it doesn't disproove this theory AT ALL. It just shows that luna/chrissy is in her little changling kingdom castle for 3 days straight (or maybe not even straight...she could have left and come back frequently). so what? maybe luna took a "vacation". she can raise the moon from anywhere, right? All she had to do was tell celestia she will be back in a few days, or maybe make up a story about defending the border for the magical surge thing.
But if you look at the part where it shows what happens right after she gets booted out of canterlot, it does seem to suggest she isn't luna. but then again, we don't know how long it took the changelings to take over that cutsy land of bunnies and stuff. maybe after it was done she transformed back and high tailed it back to canterlot. after all, we dont see luna until AFTER the wedding, which is AFTER the entire town of canterlot is fixed up and cleaned. The wedding could have been the next day, or even 2 or 3 days later! Plenty of time for chrissy to get her new kingdom in order and fly back and be Luna again.
as far as changelings go- and this is just an idea i had- what if the changelings were a race, and she didnt bring them out of tartarus (like a previous user suggested)? maybe they were just a race with no ruler, and luna came in, shapeshifted into something that looked like a queen version of them, declared herself ruler, and promised them canterlot?? Then, she would have had to not transformed back in her castle because she was not only playing the ponies, BUT THE CHANGELINGS AS WELL!
Another thought: how did chrissy send the orb to spike via royal spike burp-mail (in the comic)? That is literally only seen done by celestia. Maybe luna knows how to do it too, being her sister and all?
oh yeah, to all the ideas that luna cant be chrissy because she was a terrible cadence...duhhh..of course she was terrible. she was trying to get found out as the queen changeling to throw off all suspicion from luna onto her alter ego, chrissy. but she landed the suspicion plane at the perfect time, after she already had the shields weak and her army ready, just in time for the dramatic reveal. which makes it impossible to think that luna would be behind it. my point is, she played the "bumbling idiot villian" to a KEY!