The problem isn't really with MacGill. Essentially the fact he replaces the greatest living spinner makes it difficult for him to earn his spot.
MacGill's bowling often looks good towards the end, but his success against the tail inflates his wicket-tally in almost every match. He goes from 1/100 to 4/110, thereby making ordinary figures look like a stoical performance in the heat against all odds and symbolic of his gutsy determination etc etc etc - bottom line he is far too expensive, but statistically he looks good.
Certainly in this series he has had some ordinary days in amongst days of success, but not brilliance.
On the return of Warne you need only look at what each player offers to the team to realise the need for Warne ahead of MacGill. Australia's tail is struggling with only Brett Lee representing the good lower-order batsmen of Australia. Williams, MacGill and Bracken are generally considered number 10-11s. MacGill's fielding is lazy and quite ordinary. He also struggles to keep his bowling under control - loose balls result in boundaries.
Compare this to Warne - can take wickets cheaper, restricts runs more, can dominate the opposition, possesses greater variety and has a reputation for winning matches. His fielding is normally quite good, in the slips generally, he doesn't come across as lazy when fielding, and his batting is quite good albeit a bit rushed. A HS of 99, missing his Test century because of a failed shot to cow-corner that saw him get out.
Warne offers a better all-round player than MacGill - MacGill cannot compete with Warne's long-term success.