First of all, that wasn't Mr. Smith. He kept calling Neo Tom (he typically says MR Anderson) so it never felt like smith. Neither did Morpheus, the fact that Morpheus somehow is a Sentient and Niobi is still alive just takes away from all the prior movies. It just didn't feel like the matrix. Also I think its something with the whole Wachowski turning into a female that plays some part in giving Trinity powers from "THE ONE". Feels like she tried to add more female roles even ending with Rage Against The Machine Wake Up Cover by a female. As well as trying to connect as many pieces to the first movie really seemed like they tried to hard to achieve what the first movie did. I cant say I liked it. The ending also doesn't really show that they probably started the war against The machines again but I guess trinity being "THE ONE" as well is more important.