Please don't take this the wrong way, but my honest opinion from what I see in this post, I don't think you're going to be well received as a Commish. But if you have your heart set on it, I'll offer some advice/suggestions.
First, remember that it may be your league, but fantasy football isn't much fun to play by yourself. That means you need a bunch of other owners that consider it "their league" as well. The less it is about you having it your way, the more successful it is going to be from a participation standpoint. So while you can set the initial rules, you should allow rules to be changed by a league vote. That way it is more democratic and less of owners being beaten into submission by a tyrant.
Ok, now your topics:
1. Trade rules (as with anything else) MUST BE IN WRITING. Have a rule book. You can find basic rules on nearly any fantasy site, and then adjust them the way you want. If you really want to prevent collusion have trades in 48 hours before kickoff of the first game - owners have 24 hours to vote on the trade. Simple majority rules with the Commish as the tiebreaking vote, if necessary. Of course, this also tends to suffocate trading because people don't want to go through the hassle, and stupid owners will vote against trades for dumb reasons...not just to prevent collusion. Therefore, my preference is to just allow trades to occur and risk collusion. If owners are clearly colluding, then kick them out of the league via a league vote. Owners will use their vote with more integrity when you're talking about kicking someone out.
2. You can do a flex if you want, but if you don't want people to be able to start 3 good RBs, then I would recommend just making it a 2RB, 3WR league. Or maybe 4WR and combine the WR/TEs. Your odd RB from the same team scenario is just going to benefit one or two owners, putting everyone else at a disadvantage, which is what you're trying to avoid. Or you can do what my league does, and make QB an option in the flex. This allows you to start 2 QBs, which generally is better than 3RBs, but if you have neither at least you can still revert to a WR or even TE. Not the best option, but at least you have some hope if you're suffering through injuries and/or bye weeks. My league absolutely loves it...it's almost like a 2QB league, but you still have options and hope even if you have bad luck at QB.
3. It is up to you how you want the scoring to be. PPR leagues really don't increase the value of WRs, because ALL the wide receivers catch balls. Sure, it might increase a bit of the 90+ catch WRs, but since everyone is getting a point boost, it doesn't increase the WR value as a whole at all. In fact, in has a much greater impact on RBs who catch balls. Guys like Rudi Johnson are severely punished in such leagues. Also, it has never really made sense to me because you don't give QBs points for completions or RBs points for carries. Why give a WR points for a catch of no gain? The point is that scoring changes only benefit or hurt certain types of players (ie Westy vs Rudi)...they don't change the value of the position as a whole very much. RBs are hard to get no matter what scoring system you use, so they will be more valuable than QBs and WRs. Therefore, if you want to balance the value of the positions themselves, you have to do it by adjusting roster spots as I mentioned above.
But to recap the most important thing, you hated that league because it wasn't run the way you like it. No one is going to like your league if it isn't run the way THEY like it. Remember that and you'll do alright.