1 - You're right! - true double elimination isn't "fair"! If a player gets a bye, they are ranked as if they beat someone. When you don't consider a bye a win, you're not talking about true double elim. People are saying brackelope sucks because it ranks people according to the way a *true* double elimination tournament is ranked. I will defend that this is not the case, cuz it's not!
2 - Brackelope allows you to hold matches or redraw machines. As a tournament director you can choose to hold matches as long as you want (end of the round or until more machines open up) or redraw machines so that no one plays the same game back to back - it's not the softwares fault it tries to do things in the most efficient way possible. You can adjust the way you use it to try and insure players don't play games back to back. Often we'll draw matches as quickly as possible early in the night, then start waiting for rounds to end when it's down to 8 people or less. Brackelope weighs the machines that people have already played, so the chances of it picking a game that neither player has played increase as the tournament moves on . . . which is awesome!
3 - Double Elimination and 2-strike are not the same thing. 2-strike solves the ranking issue but you have to wait for rounds to finish.
Modifying the way your rank a double elimination bracket is exactly that - a modification - it's not *true* double elimination when byes aren't considered wins. Both have their pros/cons.
Brackelope makes things super easy and I think it's a huge contribution to the world of competitive pinball. Double elim and 2-strike have their flaws, but I attribute them to the format, not the software.