Love Borderlands and love P3. Excited to see what you come up with. If you ever need some help with concepts or ideas about tourney integration/score balancing, let me know!
Some ideas I have:
1. Use the extra P3 buttons to switch weapons. Obviously the different weapons ala borderlands would have different attributes, but they would correspond to goals on the table. IE one would score more damage to the bash toy, one would start with jackpot multipliers, etc. Mixed with P3 software, you could even do something crazy like Sniper rifle does huge damage or huge jackpots, but you can't hold the flippers.
2. Having the tourney mode separate from "story mode" - in story mode instead of 3 balls, have a shield. Each drain depletes the shield a bit. When you finally drain with fully depleted shield, get a last change shot like TOTO for an instant revive.
3. Race modes: not sure if you are a flow guy, but have race modes that are based around combos and flow shots. Basically the drag race in Corvette.
4. Special abilities: Have these available maybe once a game, or need to pull off something big to earn them. would use by hitting start button or extra p3 button. Possible abilities: invulnerability: 30 second ball save, turret or hawk: add a ball, Berserk: instant multiball but no hold flipper
5. Oxygen levels: you would have objectives but would need to hit a scoop every so often to replenish oxygen
6. Arena modes: would be like critters in P3 but with increasing amounts needed to progress to next level