I'd say the most obvious thing you're overlooking (assuming of course that I'm actually following your system correctly) is how
much better someone is at one particular stat than the next person. Yes, you're ranking them in some order, but you're not factoring the difference between #1 and #2 or #11 and #12. You're not taking into consideration how much a steal is worth as compared to a HR, or RBI. You're not factoring in how many more steals player A will get than player B, just how many players will be between them.
In the example of Reyes... yes he's #1 in steals, and above-average in most other categories. But, it's not enough just to say that he's "the best" basestealer. He's the best by XXX number of bases. The HUGE gap that is between the top couple of basestealers and the rest of them isn't taken into account. Figuring out those gaps is what leads to a successful team. Figuring out how you're going to capitalize on your strengths and finding guys to make up for your shortcomings.
I completely understand where you're coming from, trying to break down lists like this... it works in fantasy football, because all the stats go through some formula to be turned into points, all points are worth the same, and they're all added up to one number in the end, so you can compare the value of one position against another, or two players at the same position. Roto (or even H2H) baseball is a completely different animal. Here, a steal isn't worth the same as an RBI. They're not even related. Beating somebody by twenty wins isn't going to make up for losing by two saves. You're playing a much more intensive system, which takes a lot more judgement calls and massaging of your roster. It's not enough to just say that you can make up for a weak 3B with a good C, like you can with RB/WR in football, you have to maintain not only positional rankings, but rankings in each statistical category.
Add into that the length of the season, multi-position players, players going on (or coming back from) the DL, trading becomes much more interesting, etc, etc, and I think you'll find that fantasy baseball is much
different than fantasy football. No longer will your top two draft picks carry your team to the champsionship barring an injury... now you've got to put together a roster where every
player is important, even the free agents you pick up in the middle of the season.
In any case... it looks like you've got your head on right. Now you've just got to figure out how you're going to use it.