Direct control was limited to the Pale (around Dublin) and everything outside was under the influence of major Irish families, like the Kildares.
The Poynings‘ Law (in 1494) made it so that the Irish parliament could only be called and pass laws with prior approval of the king.
Henry’s deputy in Ireland, Sir Edward Poynings, failed to bring Ulster under greater control.
Increased control in Ireland would have been costly, therefore Henry relied on traditional families and the Earl of Kildare was restored to Lord Deputy.