i think that the 1000 should be a hard cap. i think that is part of the strategy. do you save some space to sign free agents/make trades or do you get as close to the 1000 limit as possible? i know that i have been bidding as though this is the case.
if you have a soft cap at 1000 that you can go over in season, what is to stop the following scenario: i have a crap team and only $750 total salary. another team is solid and has a few solid prospects that they would be willing to trade and are weak at 3b, but have $990 total salary. after season 1, Miggy Cabrera becomes a free agent. i work out a deal with the great team so that i bid 200 on him because no one else can beat me. i then trade Miggy and his $200 salary to the other team for those 3 prospects that cost say $50 total. the other team doesnt have to bid on him knowing they will get him and their salary will go to $1140. that team doesnt care if it has to cut a couple of players in the offseason, because they will likely be serious contenders for this season's WS. And even after cutting players, the scenario can repeat.
i know that it sucks for todd that he got players that he didnt think he would get because he bid high on several players on the same day, but i think that is the risk he took by bidding that high on them. i dont think that we should alter the rules we started under because someone got guys they bid on for what they bid. if anything the lesson should be that if you dont want to sign a player for a high salary, then dont bid that high salary. its not like anyone forced todd (and this is nothing againt him, it is just the example we all know of) to bid that high on several players.