I have no idea if Sakimoto went with Sakiguchi to Mistwalker or not, but Saberman is correct that Sakiguchi is a part of Matsuno's regular crew, and for me personally, due to Matsuno's direction of the game, I kinda feel that a Uematsu soundtrack just wouldn't fit it very well.
As for FFXII not being an FF title from its development beginings... I could certainly debate that.
What I do know however, is Uematsu is composing the soundtrack for Super Smash Bros Brawl on the Wii.
As far as Uematsu leaving Square is concerned, if you remember back to between '96 and '97, Uematsu had a bit of a midlife crisis, resigned from Square saying something like "he didn't want to do vgm for his entire life". Square managed to entice him back to compose FFVII, and with each of the newer FF titles his presence has gotten smaller.
And as far as Sakiguchi leaving Square due to the failure of the Spirits Within movie, I don't agree with that, as the worldwise success of Advent Children has proved that Square can do movies (even if I happen to think they should stick to games).
Personallty I think his departure is a good think, not only does it allow Uematsu to expand his composition style (I'm really interested to see how he takes to signature Nintendo tunes) and it allows Square to explore different musical venues for Final Fantasy.
I know I risk getting flamed for this, but I feel that Uematsu's work on the FF series was getting stale. The FFIX soundtrack, though nice, was nothing inspiring to me, and with the exception of a few tracks he did for FFX (Suteki da Ne, To Zanarkand) I found Junya Nakano's contributions (Besaid in particular) to be far more engaging. But then again, this is just my opinion.