I think it's just that Xemnas, like many villains, has an ego that's larger than Kingdom Hearts itself. It's like asking why Voldemort would be stupid enough to announce his grand plans for revival and then challenge Harry Potter to a duel, thereby giving him a chance to escape. Or why Sauron didn't do a better job of guarding Mount Doom, the one place where his Ring could be destroyed. Because these characters simply cannot comprehend the idea of anyone being strong enough to defeat them.
Likewise, Xemnas was probably thinking along the lines of: "I created Xion. It's my clone and I can make it do whatever I want." Whereas Roxas was an actual person that he couldn't just reprogram to obey him.
Xemnas cannot have an ego: he's a Nobody. They're nothing but an empty shell without a Heart. Therefore, incapable of feeling such.
s1britishguy
In all seriousness, this is more than a character being strong to defeat them. The
real threat is that they
leave, thus, Kingdom Hearts will remain incomplete. Sauron, and Voldemort, didn't have the option to know what's going to happen in the long run as to what they were doing. It's not like it happened constantly to know there's going to be problems and that one of their pawns is defective (they didn't act weirdly
all the time), which is where the comparison would take place. Xemnas, on the other hand, had Xion running away, going with
Riku, which I'm positive he can smell the essence of, interacting with Naminé, researching files, making Roxas question her disappearances, creating problems for the Organization, etc., etc. It's obvious where this was going. And to think that updating Xion into a machine so Roxas can fight her and whoever's the last one standing he takes (or so it seems), it's ridiculous, especially with the boy's obsessive behavior. There's just so many flaws and risks that it's just...stupid. While a villain has pride, they also don't want to fail. Why else do you think Xemnas had back-up plans?
This is the same game where Diz found out many days earlier (when Naminé spoke to herself) about what's happening with Sora, and he didn't do crap until the very end just so Xion can, in the
most contrived story telling I've ever seen, finish the year (yes, let's do something when she decided to die). Let alone have Riku choose her over his best friend after
a second meeting when the first was all "pfft, bitch, I pwned your genderless ass, if any". Yes, Riku. Whatever guilt you have, the
best way to make up for it is to let Sora sleep longer while the Organization keeps planning and possibly use Xion for more purposes. That's COMPLETE redemption right there, so smart. Riku Replica and Roxas only wish they had boobs so you can treat them the same. But they were actually written well and don't suck in and switch things like Xion does for her to fit into a story that could've been left alone. Thank God for that.
*raises hand* Oooo, I know why!
8D
YEEEEEEEEES, GLORIOUS!
*GLOMPS PLUSHIE*
Oh, if only the Organization were playable in some other, better game.