Just what did sestuna do during those 50 years? Why does he even need to go to the ELS' system in the first place anyway?
The brief contact he had with the ELS near Earth was just enough to explain to them what they were doing wrong, and how they could communicate with humans without overloading their minds. He goes to their home system to communicate with the main body of the ELS: the ones in Sol are just a colony, an offshoot. At their homeworld, he can engage in a long psychic conversation with them, telling them everything he knows about humanity and learning everything about the ELS in the process. That way the two species can more easily achieve a working alliance.
Why is 00 Qan[T] considered rivaling Turn A in the first place?
00 Qan[T] may not as powerful as the Turns in terms of raw destructive capabilities due to Moonlight Butterfly, but it's a very close second. Just think about it: In the whole Gundam multiverse so far, only the Turns and 00 Qan[T] have the capability to mess up an entire alien fleet by themselves.
Furthermore, the range of the Qan's teleportation ability is far greater than the Turn A's, and creative use of that ability allows the 00 Qan[T] to also teleport its attacks into cockpits and escape the range of the Moonlight Butterfly. Not to mention its weaponry is much more variable than the Turn A's and packs a far greater punch in terms of attacking multiple targets simultaneously (the Turn A has to rely on the Moonlight Butterfly to do mass damage, and it's indiscriminate).
Theoretically, a dense GN Field might even be capable of blocking the Moonlight Butterfly when you think about it... both operate on a nano-scale (particles vs nanomachines), thus evening the playing field between the Turns and the Qan[T] considerably.
The heavily-GN Particle infused armour on 00 verse gundams in general will cause trouble for the Moonlight Butterfly. GN Particles are exotic matter derived from topological defects, and will not play nice with things that operate on the molecular scale. Nanomachines are precision devices, and don't cope well at all with things way outside the design specs. Add in the known effects of high GN particle density on unshielded electronics, and the Butterfly might not work at all on Gundams, and certainly will lose it's instant kill effect. I'd wager a Twin Drive unit in TRANS-AM would be largely immune until TRANS-AM runs out.
The Quantum Sword is the most powerful mobile suit weapon in any Gundam series. If you leave out the Raiser Sword, it's the most powerful by several orders of magnitude. The thing is a beam saber big enough to be mistaken for a superweapon Wave Motion Gun. Remember, it's an upgrade of a ground-to-geosynchronous orbit weapon. If you fired it straight down, instant volcano. A glancing hit from it's predecessor killed the second Memento Mori, when the first one survived an entire Trans-Am condensed into a single shot from Seravee.
The ELS-upgraded version may also be flat-out immune to the Moonlight Butterfly. Technology-destroying nanites versus the ELS's shapechanging, regeneration and assimialtion is probably going to be a stalemate. Best case scenario for the Turn A in a fight with ELS!Quant is the regeneration function canceling assimilation and the ELS negating the Moonlight Butterfly.
The only means Setsuna had of communicating with the ELS was Veda: It was needed to process the large volume of information the ELS were sending into his brain. That established, how was the Veda terminal in the 00 Qan[T] able to function light years away from the Earth, when Setsuna needed to go to the ELS home world in order to understand them better?
Quantum communication is presumably instantaneous and perfect, regardless of things like range and light-speed delay.
So did... did Tieria just kinda be off with Setsuna during the 50 year time skip? Like, just uploaded to the 00 Quan[T]? Poor guy.
If, as the above question supposes, quantum communication is instantaneous, then Tieria could easily jump back and forth between the Qan[T] and Veda back in the Earth Sphere without missing too much on either end.
The ending is notorious for raising more questions than it answers, with What Happened to the Mouse abounding. The 50 years later epilogue provides us with some idea of what ended up happening to Marina (including an oft overlooked picture of her with all her grown up adopted children), Setsuna (Metal edition) and maybe a cameo appearance of Tieria. On the whole however, the only other character that is touched upon on in the Epilogue is Klaus, the girl who got half metalised, and potentially the reporter (which is either possible or lubricious depending on how innovators age. Klaus aged pretty hard). This leads us to the question[s].
What happened to Soma/Marie and Hal/Al? What was there fate 50 years on? Where did they end up.
Where is Lyle? Did he ever get over Anew? No one knows.
Did Tieria x Milenia ever actually happen? Does Tieria ever reconcile himself with being a fragment of Veda while being in some form human, which was what he spent most of 00 realising?
What happened to Louise and Saji? Once again, no one knows.
It's implied that Klaus and Shirin have a relationship. if Klaus is the XO of the Sumeragi colony ship and developed Innovator powers, where did Shirin go?
On that note, what happened to Sumeragi? The very fact that she has a ship named after her suggests that
A, somehow over the course of the past fifty years she became far more of a public figure. This could either happen due to much better public education about CB (Unlikely given the huge inaccuracies of the "movie" at the start of Trailbalzer, as they didn't even get the genders of the Meisters right). Or it could have come about due to Sumeragi doing something that warranted her getting a colony ship named after her, which leads us to.
B she's dead. You don't name ships after living people as a general rule.
The Sumeragi is entirely crewed by Innovators. This is portrayed in a very positive light, but it does raise the question- has society evolved into some kind of racially segregated Apartheid? It certainly isn't unarmed, it's called a "warship" and a suit similar to the GN archer does a fly by.
The epilogue Mobile Suit is called a Sakibure, and it's a worker mobile suit, ie, unarmed. One of the mangas does state that there was an anti-Innovator and anti-ELS revolt at some point during the Time Skip, but it was put down (in part by Celestial Being). Anyway, the reason it's crewed entirely by Innovators is that Innovators have a greater tolerance to extended periods in space than normal humans, which would practically be a necessity on an interstellar voyage (which would last years even at light speed). Further, assuming they do meet some other form of life out there, the Innovators' telepathy will be very useful in avoiding another situation like what happened with the ELS.
Feldt. This has been said before, but what happened to her?