What about PPR scoring?
And what about TE?
If you have 6 starters at WR and RB, either as 2 flex or as 3/3, that devalues QBs and TEs (especially if TEs are not flex eligible). QBs and to a lesser extent TEs would have more values if it was 2/3 or 2/2/flex. In exchange, RB and WR depth becomes more important under either setup you described.
As to specifically about having 2 flex spots vs. 3/3, it depends a great deal on PPR scoring. For example, if non-PPR, 2/2/2-flex puts a HUGE premium on RBs, so that ideally you could start 4 strong RBs. Or, if PPR, it's more balanced, with some tempted to go WR heavy. If .5 PPR, it's fairly balanced.
IMO, .5 PPR and 2/2/2-flex would create the most difficult to decide lineup decisions, and therefore maybe increase the amount of skill involved when choosing week to week (or increase the luck involved when picking week to week.... but over 16 weeks, it should even out).