The rotation isn't a mess. We've got five or six guys who can fill the back end of the rotation. The front of the rotation is missing. The bullpen is in good shape. Yes, we're worried about Story's health, the young guys, and whoever the hell is playing second. But their high ends are pretty damn high and the depth--assuming we get a real second baseman--is much better than it was last year.
Get more innings from the starters. The bullpen goes from holding it together to exceling because they're not being asked to do too much. The depth options have a floor of mediocrity instead of suckitude. We won 78 games last year, which is only 12 away from 90. Add two top starting pitchers, a real second baseman, and a RHH who can play the outfield--the hitters don't have to carry the lineup, just contribute. And if Duran, Rafaela, and Abreu end up turning into one star, one JAG, and one bust, we're in that range where we're looking at tinkering to get from a 90ish win total to a high 90s win total.
Put in a more hypothetical sense, if you imagine a perfectly average team, and replace a mediocre starter with Pedro Martinez. The team goes 25-5 in his starts and perfectly .500 elsewhere. That's a 91 win team.
The problem with teams that lose is that they ask players to do things the players aren't good at. Some of that is inevitable because baseball, but you want to minimize it. Get more innings from your top starters and your bullpen can be used more optimally. With a bullpen in better shape, you don't have to squeeze outs from a back end starter who looks like he's losing it. Better defense means fewer pitches thrown, fewer baserunners, and fewer high-stress pitches overall.