Just like LOT was a joke, so is .Link. If anything it's probably only important to introduce to us the existence of the Akashic Records, The Chrono-thingys, Schiksal's little group, AND the new and improved [The World]. It'd be happy with that.
Legend of the Twilight wasn't a joke, it was just as important to the series as Sign or the games.
Forcefully
There is no reason for wanting to wake up on her own, nor does she want to
Aura can do anything she wants, buster. I would've never expected her to go to sleep in the first place, so let's not assume her intentions.
I don't think the characters are AI nor do I see much reason for it. None the less all of them. Excluding Azure Flame Kite, the characters Kite, Tsukasa, Subaru, Haseo, and Alkaid have no purpose in being anyone other than themselves. Alkaid defended by what reason an AI would be created after her. Tsukasa and Subaru backed up with their extended histories and memories. With Kite and Haseo balanced with the poem that first appeared on CC2's site.
The poem addresses Tokio in the form of a letter, but he never received it, nor does it appear in the story. I wouldn't take it to have any plotline significance, it's an advertisement. Furthermore, Za Warudo has been known to just spit out AI players for literally no reason, such as Shugo and Rena, Sora, Subaru, the SIGN Phantoms, and so forth. The AI Theory is one of the only solutions that allows Link to make any semblance of sense.
The Chrono Core is installed inside the PC in a very complicated way. Metronome stated it to Trommel. PC means Player Character. Although this could refer to the avatar she states that the core will appear by giving stimulus to the PC while the emotional level of the PC is at its peak. If they were just AI I don't think that type of situation would apply and it would mirror what happened to Mia. Instead of waiting by having to agitate said character emotionally for the core to appear, Trommel would have probably destroyed Tsukasa there and then to get the data.
Rumor was also a PC, you know. Same with Mia, and the Azure Knights, and the Tsukasa, Sora, and Subaru AI's. They were just artificially intelligent. Plus, I don't think Player CHARACTERS have emotional levels. Possessing a human player shouldn't stop Trommel from ripping open a PC to get the Core, because it's not like it's stored in the actual human himself. The implication is that ripping open the PC, human-controlled or otherwise, will destroy or damage the Chrono Core. Both humans and AI's have emotions and utilize PC's, so this is a stalemate.
Additionally the chapter with Shugo and Rena most of you saw is actually from .hack//G.U. TRILOGY New World Guide. Its has no connection to LINK. Plus the characters in the story vanished immediately afterwards meaning if it were the same method the characters would be unstable disappear as well. There was something else I wanted to mention, however at the moment I can't recall. Anyway as I said its ones of those things that feels unlikely to me.
You are correct, but it does prove that Za Warudo does produce AI's for no reason. Shugo and Rena did vanish shortly afterwards, but that waso nly after they felt contentment at helping Aina. They chose a reason for existing, fulfilled it, and returned to the Sea of Data. The same could be said of everyone in Link, though their task is more daunting and complicated.