Eric's come onto one of the uses for such a system. Since a DM has infinite resources, what constrains him to build a series of related, and rational encounters? Besides, hoping to not turn off his players.
What prevents the DM from having the BBEG being too high level (when the DM expects the PCs to fight it)?
What prevents the DM from having too many combats, period?
What prevents a DM from having too many encounters before a healing break for the PCs?
What prevents a DM from having run-on encounters that are effectively one big encounter?
Another thing to consider, in the case of dungeons and are CR controlled areas already. Level 1 of the dungeon averages to CR1 monsters, level 2 is CR2.
From a software perspective, generic random dungeons are the easiest to automate. Stereotypically, going down means tougher monsters, so the party knows what they're getting into. Building a more traditional adventure (ex Lord Evil has kidnapped the Princess, travel through his lands, sneak into his house, beat him up, take his stuff, save the girl) is a bit trickier. Have a system to balance things would be nice.
Oddly enough, folks are bringing up stuff I wouldn't worry about. I wouldn't re-level an area the PCs have been to before, if they decide to go back, unless I actually added a new problem to be solved there. Its just not worth the effort.
Also, IF you could have the PC auto-generate plots on the fly (and keep them ready, should the PCs decide to follow plot 2 after plot 1), you don't need the game stats for all the plots, just the one the PCs are following. Thus, the fact that plot 2 is level appropriate is no big deal.
Heck in my case, I tend to design one plot at a time anyway. Not everybody runs a campaign where everything is simulated and ready to be a plot at the same time.
Janx