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I recommend using the "Ratings relative to:" function as well (if you're not already). When you're looking at your rookie leagues and even many A-class prospects, the majority are 20ovr and 20-30 potential. However, if you change your ratings relative to their current level, you can get a better idea of their current potential. And yes, potential increases and decreases often, especially with young prospects, as it does in real life. What I do is create a shortlist of the most promising pitching prospects and position-player prospects within my organization - usually around 20 position players and 10 pitchers. I base it on age, overall, potential, work ethic, and prior performance. Then once a month, I go through the shortlist and check to make sure their potential hasn't decreased, and I promote/demote based on performance and scouting changes (but mostly performance). Additionally, once every 2 months, I scrub my entire organizational roster to determine whether any prospects have been upgraded in regard to potential. If an 19-year-old prospect goes from a 40 to 45 MLB potential (as an example), and he isn't underperforming, I'll add him to the shortlist to keep an eye on him. Contrarily, if a 22-year-old prospect has a decrease in potential, and he is underperforming for a few months, I'll likely take him off my shortlist. I'm not worried about whether he makes a "comeback" or not, because if he does, I'll find him again in a couple months when I rescrub my roster, and I'll add him back to my shortlist. I let the AI run the minor league system, but I keep my shortlisted prospects on specific game strategies, and I lock them to their current minor league team. Out of your entire minor league system, only 10% will ever make it to the majors and far fewer will be stars or even have long, successful careers. There is no way to fully determine which prospects will amount to anything, which is how it is in real life. That's what makes it fun (for me anyway). That's why you need to continuously scout and keep an eye on your prospects. At any moment, you may get an underperforming prospect who starts balling out and becomes a perennial all-star; or you may get a former 1st round pick who fast-tracked through the minor league system and absolutely tore it up who flames out in AAA and never even reaches the big leagues. Just my 2 cents. Either way, you'll eventually find a system/process that works for you. It can be overwhelming at first, but once you get used to it, it's addicting!

EDIT: Oh yeah, remember to keep an eye on the scouting accuracy of each prospect as well.