Well, we are giving Shin-Ra the Sister Ray, which it did not have from the point in time we classified as Shin-Ra's strongest (i.e. pre-Crisis Core). They had the mako cannon, yes, but it's technically not the Sister Ray until it was moved to Midgar and hooked up to the mako reactors.
I've been assuming "at their best" meant giving these factions all the assets they have possessed, at the greatest strength those assets were at a time when they actually were used by the faction in question -- in other words, all their good shit.
So Shin-Ra can have Sephiroth, but no greater than he was when he worked for them. Likewise with Cloud. They also get the Sister Ray.