The main issue with FFAs is two-fold. 1) Deciding a proper rule-set for FFAs, and 2) Deterring collaboration between players.
Before I get into this, I want to note that my intent with this rule-set is to promote acting in one's self-interest. Sandbagging, teaming, or unnatural targeting are things I'm looking to mitigate or eliminate.
1) Starting with rules, stock is a very poor choice for competitive FFAs because optimal gameplay is survival and combat avoidance. Eliminate the weakest or highest % player, then repeat. Add any potential collaboration (2 players gang up on another to eliminate them) and Stock FFA can get really degenerate, really fast.
Time-based FFA doesn't have these problems. Someone wants to camp with a lead? No problem, just target the other 2+ players. You're not rewarded for camping; all it does is preserve your current state. The most degenerate thing about Time-based FFAs is killstealing, which can be annoying, I admit.
The main difference that makes Time better than Stock is that you have more choices. You can either chase the leading player, camp with a lead, or target weaker players to rack up more points. Do you target the weak player, or target the chasing players to score quick %?
1 1/2) In addition to time, players' scores should not be reduced on death (upon being KO'd) Instead, they should only be reduced via SD's. This would be a preventative measure against destroying any one player's score.
2) Collaboration between players make a life-or-death difference in Stock. As we know from Doubles, 2v1s are brutal for the solo player if executed correctly. In addition, being targeted is never fun, especially if you're losing. It's optimal to eliminate losing player before moving onto stronger ones because it's easier to preserve your stocks. Not to mention potential 2+ player camping strategies; that would be a nightmare.
On the other hand, collaborative play does not play well in Time matches. 2 players or more targeting 1 player only really works where 1st place matters the most, and even then, you can target the chasing players for points if you find the opportunity for a KO. Otherwise, the teamed players must score multiple KOs just to break even.
TL;DR Use time, not stock. It solves every problem from camping to teaming. Use +1 for KOs, +-0 for deaths, and -1 for SDs.
I'm not sure about the timer though. 4-5 minutes maybe?