For a long time, I have always applied for an EIN for every Plan I administer. THis is easy, but it does take some time.

When using one of the 401(k) Platforms such as John Hancock, ING or Hartford, they do the 1099's , 1096's and 945's using their EIN. Does anyone see any reason to apply for a plan EIN under these circumstances?

To have 1099's , 1096's and 945's for the plan separate from the employer's payroll is the only reason that I've ever applied for a plan to have its own EIN. Where John Hancock is handling those forms using its own EIN as the payor, I can see no reason for such a plan to have its own EIN (as opposed to identifying the plan by the employer's EIN/three digit number whenever needed).