As far as the suggestions system being broken... I don't think so.
The #1 complaint I have seen is the "Already been suggested". However multiple threads on the same discussion don't really hurt the system b/c Master Toad scans the board frequently.... 12 threads in a month (from different users)for one suggestion would seem to have just as much weight as one thread with 112 replies.
The #2 complaint is "Already is in the notes". This is an easy one to miss, since the notes (ranging from Reqs to bloats, to Power Goals) are both extensive, and at times, vague. Just b/c Toady has already stated in bloat XXX that he wants to add in a dwarven trash compactor (made up example) does not mean it is not open for discussion (IMHO). It is possible our discussion might inspire him in some way.
-> It does help however, if we were to get organized (kudos to zagibu ...again). <-
I love the method we are now discussing: use a thread to brainstorm, then compile a list, prioritize and poll. It'd be even better, if like zagibu said, there could be some basic automation to save on the workload.
One addition I'd throw out is that if Toady sees a few topics he is interested in pursuing, that we could run 2-3 stickied threads about just that topic. Say the next thing Toady wants to work on is underground diversity (my fav, but just an example)... sticky that topic so everyone could chime in with their ideas on the topic. That way when he is sitting down with his notes, etc...there is just one thread to reference with 176734 different opinions on the details, as well as discussion on obvious balance issues, potential exploits, synergies with related game mechanics, and opportunities for "fun stuff".
The above would work best if Toady made the thread himself, wrote a bare-bones proposal, and listed any limitation we need to know about (IE "I want to do this, but it needs to be simple" or " But I can't make any changes in X to do this, because the arc I am working on relies on that code.")
/rant