Horse trading is part of politics. If you outright ban it then effectively much like any other product the problem will be worked around either in the open or more likely just done in secret, a black market for legislations as it were.
If you really want to move closer to the goal you prescribe then you have to attack the root cause, not the symptom and the cause is gridlock. Nobody wants to pass 10 smaller bills because that'll just never get anywhere so one giant bill it is. If you want people to vote 10 times instead of one we need people in Congress who actually believe in the process and legislation.
Right now when half the legislators have it as their goal to not legislate and specifically talk about gumming up the systems, well, you get gridlock, giant riders and massive omnibus style bills.
I'm not saying that it isn't part of politics... what I am saying is that we keep hearing these bold statements about "needing transparency," yet riders or earmarks are clearly attempts to add opacity when someone tries to say, "That party is against X," because someone voted a certain way because of the riders (or earmarks). My issue is more the reason for why no riders... that being that if it is so important that it must be added as a rider to something, then it is important enough to have a standalone vote, and if you are unable to muster enough interest in a standalone vote then maybe that is something that should be relegated to the states, counties, or municipalities. The giant massive omnibust bills are a byproduct of brinksmanship. One side is attempting to get the other to fund one or more things blindly without going through the proper budgetary process and therefore withholding votes and waiting until the 11th hour with threats of government shutdowns because we all know how one party and its publicity wing will spin it, even when it is their own fault.