All of this really does hinge on the editable draft classes. The point you raise about the contracts is valid as well. That was one of the reasons I went with a traditional FBG system this time around. Each method has its own pros and cons. One of the cons of the traditional FBG ratings is that some position-specific attributes are quite low, like the average CTH of a WR/TE being 67 instead of 78 or so as it was rated in M10.
TBH, M10 probably had the best ratings system since M2003, IMO. Using M10's system as a base would be more in line with how EA rates players now, but you would get the dreaded rating over-inflation where an attribute like ACC averages 79....well above the averages for the other physical attributes (SPD 73, JMP 66, AGI 74, STR 71).
In fact, according to the data, they should all be rated on the same scale either with the same average rating (like 70 or 75 or something like that) or utilize the equal interval (where the space between each point is the same). When you use the equal interval, however, your average STR in the league goes from 70 (if you set it) to 44! Believe it or not, players are far more fast/agile/quick than they are strong on the whole, if all interval points are equal. I imagine that having more WRs/DBs on rosters than say Cs plays a role in bringing the average down as well, but that is a pretty significant drop.
This dilemma is constant. How do you accurately rate players. Outside of the game, the equal interval (let the chips fall as they may) is the most accurate. Inside the game, the M10 and M25 methods are the most accurate for getting the OVRs to be comparative to their attribute parts. The best gameplay, from opinions expressed by several users, is with the traditional FBG or Equal Interval methods.
So as you can see it is a figurative "what'll it be?" for each gamer. I expressed on this forum that if 2K throws a hat into the NFL Football Gaming ring, I would love to throw my hat into THEIR ring and push for an equal interval approach, backed by real data, of course. That could, in the future, be the real wild card. Madden's way of rating players is broken, but we have no (other) choice but to use their flawed system to rate players.
Maybe we just have to rate players crappily (sp?) in their crappy system so that we can use franchise modes and draft classes effectively. For now, however, I think we should wait to see if EA will allow us to edit draft classes. If they do, it could be full-on for utilizing a better ratings system in-game.