There's a long buildup to the question, but here it goes...
In the first Beis HaMikdash, there was a wall separating the Kodesh from the Kodesh HaKadashim, with a curtain in the middle. In the second Beis HaMikdash, there was no wall and either 1 or 2 curtains. According to Yechekel's accounting of the third Beis Mikdash, the entrance to the Kodesh HaKadashim will be 6 amos by 7 amos, which sounds again like the case of a wall with a paroches in the middle.
When describing the blood applications for the Incense Altar, the Gemara discusses at some length the different opinions for what corner should be started at. This is based on the two opinions for whether there was 1 curtain or 2, since one opinion had the Kohen Gadol emerging from the North, and the other from the South. The Gemara never discusses the order that was used for the Incense Altar applications in the first Beis HaMikdash, where the Kohel Gadol presumably emerged from the center. Given that it seems like the Third Beis HaMikdash will be more like the first, and the second is already destroyed, (a) why does the Gemara spend time discussing issues pertaining to the second temple curtains, which will never again be relevant, and (b) why does the Gemara NOT discuss how this procedure was done in the first Temple, which is more likely to have relevance to the third Temple?
There are a number of other places already covered in Yoma where a similar question could be asked, but I only thought of it here.
Michael Post, University Heights, OH
Yechezkel 41:3 states that the opening of the Kodesh ha'Kodoshim will be 6 Amos and the width of the opening 7 Amos. See MALBIM there who writes that the outer Paroches will open from the south side and the inner Paroches will open from the north like it was in the 2nd Beis ha'Mikdash as Tana Kama states in MISHNAH YOMA 51b that there were 2 Parochos.
According to this we can understand why the Gemara discusses the 2nd Temple curtains because this is how it will be in the 3rd Beis ha'Mikdash, may it be rebuilt speedily in our days.
With regard in general to the similarity between the 2nd Temple and Yechezkel's Temple, I sent an answer on 28/02/06 to Rabbi Pesach Feldman's observation on RASHI YOMA 16b DH VE'HAMOSAR who writes that the Tanna did not need to specify how much space the tables occupied because their width is stated explicitly in Yechezkel. As a rule, one can say that if we do not know that the 2nd Beis ha'Mikdash was different to Yechezkel's, we can assume they are the same.
See also RAMBAM HILCHOS BEIS HA'BECHIRAH 1:4 that I cited in the above answer, that the 2nd Beis ha'Mikdash is similar to Yechezkel's, and see TOSFOS YOM TOV in the OPENING to MASECHES MIDOS that the purpose of learning the above Maseches (which discusses the 2nd Beis ha'Mikdash) is so we shall know the measurements of the 3rd Beis ha'Mikdash, when we shall be Zocheh to receive it.
KOL TUV
D.Bloom