As always, there are larger issues at work when one is training seriously for RPS. Specifically, when one is considering training for two-prime tournaments in a three-prime world, one should consider the effect on one's local play group as a whole.
If one is a professional player (like myself, before my retirement,) and has the luxury of a trainer (or team of trainers,) the decision is easy. Let your trainers do the thinking for you; that's why you pay them. For players of more modest means, one's trainers are more often "training partners," i.e., other RPS athletes who may (or may not) be playing in the same tournament. When one trains two-prime with such players, one not only affects one's own play, one affects theirs as well.
Perhaps I can best illustrate this effect with a page from my own book, so to speak. In my early competitive days, before I had a team of trainers, I would often make use of training partners exclusively (towards the end of my career, I still had high profile training partners, such as C. Urbanus and Awesomer Thanu, but under the direction of my trainers.) As usual, I would begin training 6 to 8 weeks before a major tournament. I asked half a dozen of my most valued training partners if they would mind training in two prime with me for the duration of my training period.
This plan worked well in many ways. If one is used to playing three-prime, training in two-prime to some extent is necessary before a major two-prime tournament. However, most of one's other day-to-day matches will still be in the three-prime format. This caused much confusion in my local play group. Whereas earlier the three-prime best of three was a given, all of a sudden these matters needed to be clarified before every match. "Two Prime or Three?" needlessly cluttered up what should have been a time of quiet contemplation or boisterous braggadocio.
More troubling was that many players would experience difficulty maintaining the correct prime once it was called. A match beginning with the query "three-prime, tournament style?" would be followed by my training partner delivering two primes then shooting. This would inevitably lead to frustration, as usually there were specific strategies with which I was trying to work. Now, I realize that players intentionally drawing the foul is in vogue these days (e.g., Rob Krueger in 2003 and Lee Rammage in 2004,) but I never played the game that way.
Perhaps the best solution for the player unencumbered with a personal trainer is to train for two-prime tournaments only with other athletes training for two-prime tournaments. This helps all involved parties without diluting the efforts of the World RPS Society towards establishing three-prime as the International Standard. Take the time, play Three Prime!. If this is not possible, then playing with a limited pool of players is the ideal for which to aim. Until Roshambo Winery is successfully petitioned to change to three-prime (and I wouldn't hold my breath for this,) one must balance one's own needs as a player with the needs of the sport as a whole.