It's topics like this that make fantasy baseball INFINITELY better than fantasy football... and why it drives me NUTS when people try to replicate football by making their baseball leagues into points leagues...
Two main things that stick out as "unquantifiable" right away, whether you're playing H2H or Roto...
1.) Every league setup creates different player values
You can't create one set of values for players until you have one specific way of how their scoring counts. The second you change anything in the league setup, whether that's min-starts, max-innings, two catchers, add MI/CI, #4/5OF, one or two UT, how many bench spots, etc, etc, etc... it all changes. Likewise how you select those players can change that as well... auctions and drafts require much different preparation. Of course more experienced players usually prefer the auction because of how much freedom it provides to the owners, but the dollar values you assign to players before the auction are going to fluctuate wildly through the auction.
2.) Positional scarcity's value and a player's "overall" value only matter at certain times of the draft/auction
Anybody who's been through a few years of drafts realizes that at some point during that draft you're going to be switching gears and going from "best available" to "best available X", or "any player that can provide me with X stats". Positional scarcity really only controls player values through the first few rounds. After that the runs on certain positions come into play and owners start chasing certain positions to fill out their roster. If you're playing roto and you've got a good idea about your target numbers in each category you're right away looking at what areas you're lacking in and drafting players that will support those categories.
After only a few rounds of the draft the remaining players' values are dictated by the players who have already been selected. There's really no way to account for this numerically before the draft, it's more of a "feel" thing that you develop through mocks and such. Last year after about a dozen mocks I had a good feeling that if I didn't have 1B/3B/OF/OF/SP filled in the first five rounds, I struggled to complete a squad I felt comfortable with. It didn't matter which specific players I got, I was just never happy with my team if I went outside those five positions in the first five rounds. This year will likely be different, of course.
All that being said.... this game is all about stats. If I were to try this method (which I've attempted in the past), I would start with:
A.) Finding a "replacement level" stat-line for each position.
B.) Then I'd look at my statistical targets in each category,
C.) Subtract out the performance of a "replacement level" team,
D.) Take the remaining required stats (that theoretically separate the first-place and last-place teams) and start assigning percentages to how much each player provides towards those versus the rest of the players available at that position.
E.) Assign a standard-deviation to those players at each position.
F.) Sort the total player-pool by their value vs. their piers.
This way you'd at least limit the player pool you're looking at to about 100 to 150 players, the players that realistically need to be compared against all other players, rather than just against their own position. After you get beyond that it's all going to fall apart anyway.