Late to the party..... but after owning a machine for a little while now I think I'm in a position to comment
Firstly, I'm a fan on Peal Jam, but no - don't do that...;-) - Rear view mirror is a great shout though (could maybe swap Fade to Black out for Black?... that would actually work I reckon)
I think so far, I'd only maybe swap out The Unforgiven (for maybe unforgiven 2, or Disposable heroes.
Wouldn't mind swapping out 'Sandman too (really wish they'd given that tune a rest live, but will never happen of course), but only if there wasn't a Sandman CII mode.
If it wasn't for the CII modes and that Sad But true goes well with with the Snake multiball I'd have following (having said that, anything from the Black album does to be honest..):
Creeping Death: KEEP
Fade To black: KEEP
Sandman: Change to Harvester of Sorrow or maybeShortest Straw
Sad But True: Change to Holier than though
Unforgiven: Change to Disposable Heroes
Fuel: Have to Keep due to Fuel mode, however if I could swap ou for another Load/Re-L error track I'd put in Oultaw Torn or Ain't My B!tch
One: Keep
Seek & Destroy: Keep due to S&D mode
EOTL: Keep due to Wizard mode
Ride the Lighting - Keep I guess, although not one of my fav tunes. Swap it out for Sanitarium or The Thing that should not be
A couple of things I'd love to change are; Change the terrible CII pre-mode music to the bass intro to The God that Failed and maybe change the Unforgiven music when it's game over to Orion (although I think the unforgiven Intro works great as it is)
Would actually be great if there was a way of just adding tracks to the game without taking any away, however I understand that this wouldn't be possible (without I'd imagine some coding)
p.s: I'll likely revisit this later and just list all the track which I wish were in it (and potential modes which would fit with them.... he he)