I agree in large part with everything you said, but I have issues with everything I bolded.
Clearing cap penalties? I've seen this comment a couple of times over the past...maybe if users didn't spend like the freaking Yankees of football and ignore the salary cap, people wouldn't be asking for this.
You already can front-load contracts...so idk what game you're playing. Scouting is already extremely easy and its possible to know exactly who is and isn't going to be an excellent player before the draft, if anything they should make it harder so my team doesn't end up 99 OVR in 2 seasons like it does now (if I don't have house rules of some sort with the draft.)
You also can override trades...with the "force trade" command and 32 team control. Plus, most of the things you ask for here make it a more realistic experience, this feature doesn't fit with that at all.
Draft prospects can't go in the same order every time as the teams who are picking in a certain order are always different. I'll agree that the import logic from NCAA needs some work, but that has no bearing on the Madden classes (and since you didn't specify, I assume you meant ALL prospects.)
That one is called TAMPERING and is against NFL rules. You can't negotiate with players that aren't free agents yet, unless they are RFAs (and even then you still have to wait for free agency to start.) And if you absolutely must have it in your wishlist, and this can happen to the other teams, you most certainly must allow it to happen to you as well...anything other than that is just a person wishing their team could be a Pro Bowl team every year.
RFAs are expensive, and always will be expensive...its tough to pry away a desirable player from a team and since they can match your offer, the only way to get that player is to spend a lot of money.
As for this, why would we have them take out something that they just put in, and something that has worked well in the FIFA franchise (granted in FIFA its called something different, but the function is basically the same.) Give them time to work on it a little bit.
And getting rid of factors like consistency, clutch, and confidence makes the players less human and more robot, which is fine if you don't want an accurate NFL simulation...but if you do, you want there to be a noticeable difference between an unproven rookie's play and Tom Brady's (without having to unnecessarily drop physical or mental ratings to make the rookie play like a scrub.) Let the rookie or unproven/inconsistent player have their flashes of greatness, but also their horrid stretches so they can earn their stripes and have those ratings grow or fall based purely on performance.