To change the default font size (Note: this will change the settings for
tooltips in Excel and other programs) --

    Right-click on the desktop, and choose Properties
    On the Appearance tab, click Advanced.
    From the Item dropdown, choose Tooltip
    Choose a font Size, click OK, click OK
        (Note: selecting a font type here will not affect the
           default font used in Excel's comments)
    You can also set the font to Bold or italic, and select a colour

To insert a comment with a specific font type, you can use a macro:

    http://www.contextures.com/xlcomments03.html#Formatted

How about using the add-in which have following code in standard module.
(This add-in changes only cell's context menu.)

Option Explicit
'
Sub Auto_Open()
  On Error Resume Next
  SendKeys "{ESC}"
  Application.CommandBars("Cell").ShowPopup
  Application.CommandBars("Cell").FindControl(ID:=2031).OnAction _
    = "MyComment"
  On Error GoTo 0
End Sub
'
Sub Auto_Close()
  On Error Resume Next
  SendKeys "{ESC}"
  Application.CommandBars("Cell").ShowPopup
  Application.CommandBars("Cell").FindControl(ID:=2031).Reset
  On Error GoTo 0
End Sub
'
Sub MyComment()
  With Selection.AddComment
    .Visible = False
    .Text "Comment:"
    With .Shape.TextFrame.Characters.Font
      .Name = "Times New Roman"
      .FontStyle = "Normal"
      .Size = 11
    End With
  End With
  SendKeys "%(IE){ENTER}"
End Sub