When the developers originally created the ability to jump over your opponent, cross ups were obviously supposed to be in the game. Over the years most 2D fighters have had some sort of cross up feature and it is basically a FG staple, not a flaw in the system.
As for your second paragraph I have no idea how that relates, and it is kind of funny you complain about frame trapping when the block button system puts a greater emphasis on frame traps and chip damage. Not to mention that block button leads to actual unintended affects like the meterburn glitch, variable block stun, etc. So if you really want to compare the two in terms of NRS games, the block button has caused more "unintended" consequences than the back to block system has.
As for B2B being garbage for fighting games, that is pretty laughable considering most FGs use it. BlazBlue, SF, MvC, Tekken, Skullgirls, Persona, Injustice. Not that a block button is bad, it has its pros and cons too. But just because you prefer one over the other does not make one "trash".