All i have ever read when this topic comes up in other threads are people's lame references such as "I heard from someone" or "I think that" or "I read somewhere" when it comes to assertion about the the 27 true runes are equal in power, they just express it differently or it depends on the will/power of the bearer or other comments along those lines. And while those maybe factors i don't think they can negate the former idea that some of the true runes might be stronger than others. Because, as far as in game goes the evidence a lot of the time seems to be contrary to the idea of all being equal. I mean the Rune of Beginning through its 2 aspects, kept the Beast Rune at bay for long time (via Jowy's part of the rune) and resisted the Blue Moon most power magic attack of a 100 blood sacrifice according to Neclord (via Riou's half). Why would Windy be only after the Souleater. She could have easily got another true rune if their all the same in str. Yes, at some level i am sure someone will say "well the nature of the souleater appeals to her evil personality" blah blah..at some level yes, but more realistically i think she is attracted to power, and feels the souleater is seemly more powerful than most given its ability to harvest other ppl souls. And who could forget Leknaat's famous line which has been debated as much as the day is long, being that the sun rune has shown itself to be especially powerful even among the true runes. etc etc
So summarizing my rant, unless someone can show me a quote/statement from Konami, Yoshitaka Murayama, or some official magna or other document, i see no reason to believe the assumption/rumor that all trues runes are equal when aleast the in-gameplay seems to suggest a few might hold the potential for more power.