This movie should have been a prequel to Desperado.

I get the feeling Robert Rodriguez wanted to (or was encouraged, by say producers to) revisit the Mariachi character (played by Banderas) but felt confined within the already established canon. Also he wanted to tell a broader story that encompassed bigger elements like the liberation of Mexico. For the sake of story flow certain elements needed to be presented a certain way (or so he felt) hence the killing off of Salma Hayek's character, which I thought was a huge mistake.

Killing her off was a disservice to fans of Desperado and also was a repetitive story telling device.

However I think by placing this film before the events of Desperado you could free up the story a bit make the film feel a little less disjointed. Obviously you would need to change some things to reflect that this took place before Desperado and no Salma Hayek (although you could tell the story in a flash back sequence, I don't know).

P.S. I've never seen El Mariachi so I don't know how that movie fits in the trilogy.