A)Different hair color/style, B)he talks, C)he's wearing glasses, and D)he just doesn't look the same. And is it me, or E)is it kind of weird to have a guy with a version of himself from like 20 years ago right next to him. F)I get the feeling they would have said so if he was Crono.
A) Miguel and Crono both have red hair, Miguel just ties his back
B) Crono was not mute, only a silent protagonist. Serge also has speaking lines in this game when Lynx controls him, so it's been established that "silent" characters are able to talk.
C) "Clark Kent wears glasses, so surely he can't be Superman!"
D) That can be part of how he aged and how he's drawn in Cross. The ghost children don't look anything like Toriyama characters.
E) And nothing else in this game is "weird"?
F) Unfortunately, this is the part that really does make Miguel not canonically Crono. HOWEVER, while it certainly shouldn't be put forward as truth in the Encyclopedia, if someone were to say Miguel is Crono in some sort of fan work, I don't think it would really be reaching too far.