Yes, he is.
And really, Neo had to die. It didn't suprise me one bit. He was "the one". It's clearly a Jesus analogue. Neo had to die because that's what martyr's do. He "died to save us from our sins". The sins in this case being the machines.
Trinity was a bit...I dunno. I knew as soon as they crashed that she was dead, but I think it would have worked better if she'd lived.
I thought it was better than the 2nd movie. The first is still my favorite by far, but all in all this one was enjoyable. Yeah, they took it to the extreme with the battles and stuff, but that's Hollywood for you.