Why does Michael change the protocal of the family??

Tom asks Michael "why are you cutting me out of the action?",and then Tom mentions "and why does Neri report to you instead of through me or a caporegime?" At first I didn't give that line much thought, only that it was a precursor to Michael's bold: you're not a wartime..."line.

My question is this: why was Mike changing the family organizational structure? I thought that was the safest measure of security for him?

Wouldn't it make more practical sense to have Neri report to Tom?

The novel does explore this in more detail than the novel. Tom isn't a wartime consigliere so he is removed from that position because Michael feels that things can get rough with the move that they're trying.

Neri is also supposed to represent Luca Brasi who reported directly to Vito.

Also, Tom was Vito's choice. Neri was Michael's. Tom was part of the bargain Vito made at the Dons meeting.

...and, at that point in the narrative, Michael needed Tom to be completely divorced from what was about to happen in NY, so he could be effective as Michael's "legitimate" lawyer for his new "legitimate" career as a "legitimate" casino mogul in Nevada.

The more think about it, it seems Michael wanted Tom completely out of the Family, period.

From the final Vito meeting, until when he embarrasses him in front of Neri and Rocco, its obvious...he doesn't need Tom anymore.

Louren, I disagree with you!
With Sonny dead, and Fredo being the imbecile that he is, Michael needed people he can trust, other than Al Neri or Rocco, who by Michael's own admission in GFII were "Businessmen" and that is where their loyalty lied.

I think there were 3 motives for keeping Tom out:

1- His "Face Value" announced reason as declared in GFII after the Lake Tahoe shooting sequence; to preserve his faith and trust in Tom by making it clear to everyone that he knew nothing about what was going on, so there would be no attempts at Tom's integrity (as apposed to Fredo's for example).

2- Tom was Consigliere to Vito, was older than Michael, more experienced, and contradicted with him in cases, while Michael wanted to consolidate his power in times of crisis, the last thing he wanted was someone second-guessing him every step of the way (eg. the boathouse sequence in GFII when tom asked Michael if he really needed to wipeout everyone?).

3- Finally, Michael needed to dispose with the middlemen in order to have the move fully under his control; Tessio and Clemenza were unhappy with the way things are going and thus susceptible to "seduction" (true with Tessio) , and hence he needed Al Neri to hire people and report directly to him in order to get things done.

Michael loved Tom, but Michael needed to get things done his way; and in his usual calculating method, he found the best way to tackle the "Tom issue".

Oops.