I'm only in my second season, but my farm system is stacked right now. Discounting the couple created prospects I put in there, my pitching is killing it...AAA starters have approx combined ERA of 2.20 and combines WHIP of 1.15. My AA starters have combined ERA of approx 2.90 and combined WHIP of 1.25. I'm pretty decent offensively and I'm versatile in my positions. I've got 7 or 8 guys who can effective if needed to fill a MLB hole.
Basically what I did was the first thing I did in my first season was looking through the free agents for depth players. I picked up 2B Mike Freeman who was a solid utility player. I found another utility player in my system that could be on the main roster. And I bolstered by bullpen by picking up FAs SP Foltynewicz to by my longman, RP Ryne Harper as my middle inning guy, and RP Rosenthal to by my setup man. This allowed me to put arms from my MLB bullpen down in the minors to bolster those pens, plus give me good depth.
I focused on scouting and hiring better scouts. I released a few low-levels players and signed new FA prospects with decent Potentials and stats. Whenever I made a trade, like Reese McGuire and Hyun-Jin Ryu last season, or Kikuchi this season, I try to get multiple prospects for them. Foltynewicz proved so reliable as a longman and temp 5th man that in Season 2 he's my 5th man. This made Kikuchi expendable (even traded up when CWS offered me Dylan Cease for a song) and so him and Kirk were traded for prospects. Also moving Folynewicz to #5 opened up a spot so I signed FA Will Smith, who is putting up ridiculous numbers.
After my first season I lost a bunch of my system players because I didn't resign so then I just signed like 20-25 replacements with mostly B/C potential, and some As (who were usually like 50-60 OVR) from the FA pool to go along with my drafts picks (my first round pick went right on my main roster). I'm at the All-Star Break and AAA team is 56-28 and my AA team is 45-36. So what I'm doing is working.
I think the simple advice I have for anyone is this:
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If you have a weak position (like me with 2B) STOCK UP on 2B. You want a lot of options to choose from over the next few seasons.
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Decide you who want to keep going into free agency well beforehand i.e. you can't afford to sign two guys, pick one, stock up in the other's position.
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Comb the Free Agent list for players with good potential. Honestly, anyone with a B/C potential is good value. Check out their attributes to find ones that best suit your needs. I myself concentrated 2B and Outfield (and pitching, obs) and the stats I cared most about were having decent speed, left-handed or switch, and that my 2B had good fielding and my outfielders had good arms. Then I sign say 3 OF with good arms and decent speed (50+), but one specializes toward contact, one toward power, and another toward defence.
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Use Training to bulk up deficient stats on your prospects.
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Pay close attention to your scouts and their assignments being up. Upgrade your scouts over time.
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Take the time to construct your AAA and AA lineups. If you're just auto-fixing it constantly, then you have no control over the playing time your guys get or optimizing them. You don't want someone with 65 Contact and 70 Power against righties only in the line up against lefties, when he has 35 contact and 30 power against them. ---Make sure your bullpens have at least 1 Starting Pitcher in your bullpen and you have high velocity set up/closers---monitor your pitchers month-to-month...if your #4/5 starter is floundering, move him to the pen and replace with the SP in your pen.
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Make sure you sign versatile players. Someone who can only play 1 or 2 positions needs to have some really good stats for me to justify it. Signing players who can play 3+ positions is great. And you want a few of these guys on your MLB bench and all throughout your system. It makes plugging in injuries and balancing playtime pretty easy to manage.
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Look for catchers who can play a secondary position...I have a catcher in my minors...he's only a D potential and 61 OVR, but he plays 1B/2B/3B secondary, making him very valuable in terms of injury replacement. I have a second catcher who is a D potential and 62 OVR, but he can also play LF/RF. These guys will never make my MLB roster, but are godsends when it comes to team system management.
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Really evaluate your players in your system. When I started up this season, I found Samad Taylor in my system. D potential, I think he was like 68 OVR when he started. I needed a utility bench player and evaluating him as such, I realized he had a lot to offer...he had 80ish speed 50ush steal, 50 BR AGG (I needed speed and stealing so now he's a good pinch runner too). His fielding stats were all decent with pretty high reaction speed. He's around 40 for POW and 50 for CON, so I put him on my MLB Roster. Now he's a 73 and is basically and every day player since he can play the entire field except 1st. He's added so much depth to my roster, that combined with Berti and Biggio between the 3 of them I have every OF/3B covered 3 ways, SS covered twice, and 1B covered once. My main utility guy in my system 2B Mike Freeman (was on my MLB Roster last season) can play all 7 positions---Having guys like this are perfect injury callups since they can fill any roll whenever, and don't leave a huge gap in the system, since they are replaced by another guy this that.