Mega Man X for iOS received a small update today: the game is now fully compatible with iOS10. It runs significantly better on up-to-date iPhone firmware - crash free! What's more, a blue border has been added to the left and right side of the screen. This was done to accommodate iPhone 6, iPhone 6s and iPhone 7 resolution.
Unfortunately the game still plays as good as you remember. I can't recommend this particular port; you're better off with the 3DS Virtual Console version!