is there a special consideration when chosing a 2 phases or 3 phases control softstart
The only possible advantage of a 2-phase softstart is a lower price.

Assuming that there is no electromechanical bypass contactor, the forward voltage drop of the SCR's introduces a slight voltage imbalance. That causes a  current imbalance that is larger than the voltage imbalance, but still small. However, there will be some increased heating in the motor.

If one SCR shorts, the motor will continue to receive single-phase power until the a circuit breaker, fuse or disconnect switch opens. With SCRs in all three phases, that would only happen if two SCRs in two phases are shorted.

There is also this from an Eaton Corp. publication:


  The asymmetrical trigger control developed and patented
  ... by Moeller, an Eaton brand ... avoids DC components, which normally result on a two-phase–controlled soft start controller. Asymmetrical trigger control suppresses the formation of an elliptical rotating field, which leads to uneven stresses in the motor and extended acceleration times. ... this asymmetric trigger control is active during the start and stop ramp.


Consider:


Is the cost of the 2-phase model a little less than the 3-phase?
Is the motor duty less than operating 24-7 right at full-load?
Are you concerned about a loss in efficiency that you can probably not measure?
Are you concerned about the consequences of the failure of an SCR? In other words, what is the worst that can happen if someone presses the stop button and the machine doesn't stop?
Do you have any worry that the motor might not last longer than the rest of the equipment?


There are many situations in which it makes perfect sense to buy the less expensive alternative.