I'm pretty excited about the lower levels of our second basemen, but that's not to say that everything is roses. There's a good chance that the entire upper two levels of minors turns over completely by the end of the year (save Watkins, who might actually graduate to the majors by the end of 2013).
Filling those gaps will be some exciting names, though. One in particular to look for his Gioskar Amaya, who is one year away from being a Top 100 consideration.
The league average wOBA for a 2nd baseman last year was .302.
Darwin Barney is an interesting player. The organization will tell you he's part of the core, and defensively that might even be true. On offense, though, he's about a full standard deviation from where he needs to be. You have to be Ozzie Smith reincarnate to compensate for a .299 OBP, but Barney did provide some value at the position last year through his glove. He's projected for a modest increase in wOBA (to .292), and that's livable when the average hovers around .300. All things considered, Barney is an average 2B for a below-average price. That has some value.
Adrian Cardenas has usually always brought the lumber in the minor leagues, and for one reason or another never really got a fair shake in the bigs. He's a minor league FA, so I don't know where he ends up next season, but if you think he's got no future as a starter in the majors (the Cubs obviously think this) he's probably got some value as a utility infielder. Depending on how the Stewart/Valbuena battle ends up, Cardenas could easily see a MIF future on the Cubs next year (40-man options right now: Lake/Watkins/Villaneuva/Vitters). Alfredo Amezaga is old, and terrible. He's one of the roughly googol signings the Dodgers made this offseason, so he's their problem now.
The future is bright for one Logan Watkins. I'm not too sure why he doesn't get more press: he is relatively young, takes his walks, has average power for the position, and has done all of those things consistently for 5 years in the minors. SSS warning here, but he also just finished eviscerating the AFL this year (over 40 PA, so take it extremely extremely extremely lightly). He's seen time as a SS and CF and even some 3B, so he's a good bet to be a utility infielder in 2014 if he doesn't win that job outright in 2013 (or even 2B if Barney is traded/bombs). Nate Samson must be bald or something, he doesn't have any power to speak of (that's terrible, I'll show myself out). He signed on with the Reds to languish in their middle minors next season.
Ronald Torreyes was part of the Sean Marshall trade (alongside maybe sexist Dave Sappelt and Travis Wood), and he's been just sorta okay (considering how good he was B.C.). He's still only 20, but struggled pretty badly this year in his first taste of A+ ball (relative to his other seasons). He's a real boom/bust BABIP guy (never between .275 and .370 in his career), and he puts the ball in play a TON (low walk rate, very low strikeout rate), so he's got lots of chances for luck to play a factor in his game. It's really odd that his BABIP so wildly fluctuates given this fact, but se la vie (and SSS). He was hit-unlucky last year and still was better than the average 2B while being league-young, so don't get the wrong impression; I was just expecting him to torch A+ and he didn't.
Zeke DeVoss fell to Earth pretty hard last season, but the fact that he maintained a .354 wOBA over 581 PA is still very impressive. He's not young relative to his league, but he's still a 2011 draftee, so he's got plenty of time. He's probably 3rd on my list of 2B Cubs prospects, but still a good one nonetheless. He might not stick at 2B so a change to CF (and a diminution of his status) might be incoming.
Gioskar Amaya might be the best 2B prospect in the system (though Watkins is definitely more likely to make it to the big leagues). As a 19-year old in A-, Amaya slugged .496. That was good for third in the Northwest League: 1st and 2nd were a pair of 22-year old corner infielders. His K% rate is a major flaw that will need to be addressed before he turns into Brett Jackson, but he's a slick fielder that hits for average and power. That's a pretty nice combination.
Daniel Lockhart hasn't impressed since being the 10th round pick in the 2011 draft. He'll be 20 this season, but in his first 2 Rookie League seasons his number indicate that he was very outmatched. He's still young, but doesn't look at all promising. David Bote had 150 PA in rookie ball this year and did pretty well (as well as a .226 average can). He had gap power and drew his fair share of walks. He's got a long way to go, but as a 2012 draftee the world is still ahead of him.
I haven't done enough research on all of the other positions, but I'd be surprised if there was another position the Cubs were better at then 2B (excepting CF, maybe). They don't have a Baez or Soler at the very top of the list, but the depth is really astounding (and I consider Bruno to be a 3B. If he sticks at 2B, that's another pretty intriguing prospect). Just glancing at other people's lists for prospects, it really does shock me how little love there is for Watkins. He strikes me as a low-ceiling, high-floor guy, where you don't think he'll ever make an all-star game but wouldn't be surprised to see him log productive time for a dozen years. I'd order them Amaya, Watkins, DeVoss, and Torreyes (though DeVoss is a real threat to go to CF).