FFAs pay too much. I know this statement may be unpopular, but it is a problem. Sure, everyone enjoys the high payout, and it's a great and easy way to make money, but why do we want to play in an RPG in which it is easy to advance in (acquiring more mons/TMs)? It's like having a system where it's really easy to get Pokemon *coughtnationalpark*. This problem is further exaggerated by the frequency of FFAs. They happen almost everyday, sometimes two times a day. People can make money easily and too quickly.
Furthermore, payout is not relative to the skill or tactic involved in placing high in an FFA. You shouldn't be rewarded as much in a style of battle where luck, chance, and simple diplomacy are the contributing factors to winning instead of strategy. To win FFAs, it becomes less about eliminating others, and more about others eliminating each other for you, while you sit back. A common way to play involves setting up Substitute and buffing your stats, while hoping not to get attacked in the process. Here is another thing you can do: Contact everyone in the FFA and ask for a truce. Almost everyone will accept, and you are almost guaranteed to get a high position. It will be interesting to see how effective this is as more people try it out. However, my point is that it doesn't take much thought to win or place high in an FFA, and therefore you shouldn't get as much money as you do currently. Look at this battle; Stinky (Michael) got third place and $14,500 using Wobbuffet. He just called random Mirror Coats and Counters. I know this kind of stuff is unavoidable, but it's further evidence that FFAs can pay too much money in relation to effort. Yes, time is spent in an FFA, but most of it is spent waiting or insulting Near.
My proposal for payment is 500 for the first two people out, 1000 for the next two people out, 1500 for the next two people out, and so on, except first place gets an extra 1000 than they normally would from this pattern.
As for refs, they are overpaid as well. They get twice as much money for reffing a battle with the same amount of Pokemon. In a 6 VS. 6 battle, a ref is paid 3000 for reffing a battle with 12 Pokemon. In an FFA, a ref is paid 6000 for a battle with 12 Pokemon. Refs should be paid 500 for every 2 Pokemon in the battle. If there is an odd number, ignore the remainder for ref payment.
I also think FFAs are diminishing the frequency of normal battles, you know, regular one on one battles. You do remember them, right? Heck, even more double battles wouldn't be that bad. Single battles are really the heart of Pokemon, and Pokemon was designed to be played in singles (and doubles later I suppose). FFAs are our own creation, and they can be fun and all, but the moves and abilities don't support FFAs as much as they do 'normal' battles.
Another thing about FFAs I would like to discuss are rule decisions. I'm sure we've all seen some really crazy, bad, or fun rules. I'll admit to making some of the bad ones. However, one rule I never use is Auto Taunt. The main problem with Auto Taunt is not that it takes away from the strategic aspect (what little there is) of the battle, but that it makes the FFA incredibly simple and easy to ref; therefore, it makes the battle overpaid even more (for the ref at least). Another bad rule type I'd like to discuss is one that enables you to use Pokemon you don't actually own in your stats. I don't think this type of FFA has occurred anytime recently, but it seems like it's deviating very much from the URPG, and the collecting, working your way up aspect of it.