Len Mansky responded:
> This only deepens the mystery. * Why* did the constructors of the Second
> Temple not follow Yechezkel's plan? Technical reasons? Do Chazal say? If
> we were to build a Third Temple soon, im yirtza Hashem (Gd willing),
> would we use Yechezkel's plan?
To the best of my knowledge, the Zohar Hakadosh (Pinchas) explains that
Ezra and Nechemiah knew that Yechezkiel's plans were for Mashiach's
(Messiah) Temple and therefore designed their own. Some of their design
considerations can be found in the Talmud. The Zohar says they hoped their
Temple would be temporary, hoping that Mashiach would come.