Some plot holes?

Saix knows. Both Saix and Xigbar have a piece of Xehanort's heart in them. Isa doesn't know about the plan
As for specifically why Saix asks for a heart when he is defeated, there's a scene in KH2 where he asks Xemnas if he can "end this charade"
Saix was acting when Sora beat him

 

I would just like to point out that they were talking about Sora's memories and by extension the Keyblade. It's also said by Isa in days that he is trying to figure out Xemans true goal. So he knows the intentions of the group when it comes to Xion. As for Why the apprentices still trusted Xemnas, there are a few possibilities. One is that people are just that corrupt. A more likely one is Xemnas line in another scene of days: "Never again will it (The heart) rule us." I think that basically, the other members believe that he did this because the darkness controlled his heart and therefore his actions. They probably just forgave and forgot and are working together with him to get their hearts back. Allot of these aren't actually plot holes; they just aren't clearly stated. For example: Ansem didn't have an easy time with the door to Kingdom hearts. He created it artificially, like Xemnas did. What's different is that he used the hearts of the worlds that the heartless had destroyed. Then he used the portal in hollow bastion to get their. (The keyhole from the seven princess' hearts) If he had actually that easy of a time getting to KH, the worlds would have been screwed before the game even began.

 

-If Terra-Xehanorth unlock the original 6's members hearts, transforming them in nobodies, then why they are loyal to Xemnas, and they call him The Superior, showing how much respect they have for him? Shouldn't they be suspicious of him?
Probably they didn't knew they would become nobodies.. they gained power using darkness, becoming a nobody was a side effect, probably not even Xehanort knew about nobodies, he just was using the darkness to make people lose their hearts so they can be filled with his own, not until after they discovered they have become Nobodies, by that time they had to trust Xemnas (the one who knows most of the misteries of the heart) to "fix them", half of the org was also controlled by Xemnas because of they had Xehanort's heart inside of them.. but the other half had their own agenda (as seen in CoM), but used the organization to achieve their purposes
-If "Ansem" SoD opens relatively easily the door to kingdom heart, then why Xehanort needs the X-blade? And if in BBS the X-blade was created from the light and darkness of Ventus and Vanitas, then why now to create the X-blade a new keyblade war is needed? I just don't understand
Both of these attempts didn't work, sure we could argue that it didn't work because the heroes of the light were there to stop him, but we could also argue that it didn't work "because it couldn't work", if you do not achieve kingdom hearts by the "right way" maybe every attempt is doomed to failure, Ansem SoD was crushed by the light of kingdom hearts, the X-blade was broken by Ventus.. after all this Xehanort made a plan that is more suitaible to happen, but that was only possible after he recovered data from this other attempts, much of the information of the "Keyblade war" is lost so he had to make experiments.

-If Terra (I mean Lingering Will) hasn't a heart, but only a mind, then why he can wield the keyblade?
The Keyblade is show to have some kind of "will", it changed hosts in KH I (from Sora to Riku, than back), so It is possible that the Lingering will and the Keyblade will was the same, that is also why the Keyblade has gone to the dark realm to protect Aqua.
-Why after the explosion of the machine for encoding kingdom hearts, Riku return normal and Ansem is sent to the realm of darkness?
"Anything can happen" we can't know unless we know all the "science of kingdom hearts universe" something that I accepted as true is that: Riku had already accepted his darkness and had domain over it, Ansem like everybody else that had been exposed to the darkness could wield it, but was "slave to it", the machine made the "darkness go back to the realm of darkness", so Ansem was lost in it, Riku who was in control of his own only lost his form as Ansem.. you could also argue that the effects of the explosion were more severe in Ansem because he was closer to it than Riku
-How was Xehanort's Heartless able to mantain is own mind?
It is stated by CoM and other games that Sora and Xehanort were capable of maintain their minds because they accepted the darkness, they became heartless of their own volition so their hearts were not lost, even though covered in darkness other people were devoured by darkness against their will.
-How is possible that Roxas and Naminè co-exist with their somebodies? They are also special nobodies, the first is able to wield the keyblade and the second can modify the memory of Sora and of the people linked to his heart. Plus they are the only nobodies who can fell real emotions since they was born.
Your question anwnsers by itself: They were special. Sora had two hearts so one of those was kept by Roxas (ventus' heart) and the other became a heartless, Kairi's heart was freed as well ,but she didn't had darkness in it so she could not become a heartless.. because she was one with Sora by that time his "heartlessfication" made freed 3 hearts and made 2 Nobodies, all of them were linked together.. because Naminé was Kairi's nobody , but she was Sora's as well she had her power over Sora, and people conected to him.. every nobody seems to aquire some power when they are born, that was Naminé's.
-Why Roxas loses his memory after being captured by Riku?
That is why DiZ kept Naminé alive.. after he was finished with her, he asked Riku to kill her (which he didn't), She made the same thing with Sora, Donald, Goofy and Riku's replica.

-How in CoM Sora, Donald and Goofy arrive at Castle Oblivion?
The castle seems to have some power to attract people to it when they need help... maybe Ventus' body sensed Sora? The same thing happened to Riku and Mickey.
-Why Xemnas can't use the keyblade? If Roxas who is Sora's nobody can use the keyblade, then Xemnas who is the nobody of a keyblade wielder should be able to use the keyblade too, shouldn't he?
When Xemnas was born (as Xehanort) he was confused about his identity because Terra and Xehanort were fighting inside of him.. he didn't knew he had the Keyblade even though he used it twice (once to open the keyhole of hollow bastion, and to take the hearts of the organization). We know that Xemnas has some memory of Terra (like his friendship towards Aqua.. but one can say that he only remembers her because she appeared to him after he was born as Terranort).

Maybe we should consider "Terranort" and "terranort's heartless/nobody" a different being from Xehanort as he is made of Terra as well.. the confusion of these two hearts made a new persona.. even though it shares more traits with Xehanort.. so he doesnt know every time what he is capable of... maybe Xehanort time travelled and said to him of his powers to control the keyblade , but after Xehanort was gone he lost his memories (including of being able to use the keyblade)
-Why Terra-Xehanort in KH2 has Xemnas voice and red eyes, while in KH BBS he has yellow eyes at first and red eyes after losing memory and Ansem SoD voice?-Why Xemnas when he goes to take Roxas into the organization has YELLOW eyes?
The eyes are a indication of being dominated by darkness, due to going to the dark realm or other methods.. by the time "Terranort was born without memories"(after he fights with Aqua), he must have been cleared of darkness so that is his original eye color? Or maybe the mix between Xehanort's eyes and Terra's.. but he recovered his yellow eyes after becoming a heartless... I didn't notice the voice though.

-How can the organization know about Naminè's powers?
They captured her and made experiments probably.
-How can Xemnas know that Sora has become an heartless and that Roxas would have born inside Twilight Town?
Some of Xemnas knowledge comes from the future.. but also all Nobodies are born in "worlds in between" like : Castle oblivion (Naminé), Twilight town (Roxas), and maybe the tower of Yen sid (but we don't hear about any nobody being born here).
-If Sora becomes an heartless when he unlocks his hearts, then why when Ansem uses the keyblade of hearts on Maleficent she only transforms into a dragon?
That keyblade had the power to free the darkness of one's heart, by doing in Maleficent she became more powerfull , but Sora used it to take his heart and free Kairi's.. the same logic goes to Master Xehanort taking away the heart of Aurora, but spliting Ventus' heart between light and darkness.. the same tool can be used in two smilar ways.

 

Honestly I feel that these plot holes are more like questions that have either been answered via game, or will be answered. I mean we still have one final game to be released which is supposed to tie up the Xehanort Saga. Any plot holes we have as of now, I'd just shrug it off because at this point...anything goes with this series. (Within the games respective boundaries of course)

 

Maybe this is one:
How can Nobodies remember who they once were when they don't have any hearts? CoM established that memories are contained within one's hearts and even though Nobodies can re-obtain their hearts it still takes time. Although most Nobodies are created and still remember who they are despite not having obtained their hearts yet.

 

It seems like memories are stored in the brain, but connected through hearts

 

It is established in Dream Drop Distance that Nobodies will obtain hearts of their own over time, having Xemnas just be a big liar because he had other motives. Looking at that, I think back to Days, having just played it recently. When Roxas starts out, he doesn't know anything; it may be said he doesn't have a heart. However, as the story progresses, he gets flashes into Sora's memories. I could guess that this is the heart being crafted.

Personally, I do not get anything about the whole time travel thing in Dream Drop Distance. It just makes absolutely no sense, and complicates an already complicated story.

 

Yeah, it's really very confusing the whole time travel thing, but Xehanort says that thay can travel only if they leave their hearts behind, so thay should travel only with their hearts, so how XIgbar, Saix and Xemnas time-travelled?

 

It's not really clear, but it seems to have something to do with Young Xehanort, who was tasked with gathering the 13 forms. Alternatively, another of the rules is that these people need to move linearly through time, so it's possible that all these forms actually gathered an waited for this exact moment. It's even possible that these are all from the future and we'll see how they return in KH3

Or, y'know, Timeless River