Lets take an average DD now. They're probably all within 5% of each other (all things being equal). Most DDs are going to be in that 90 empy, 99 Oat GS, 99 TP bonus GK range. Substituting with a 99 R/E will give you, at best, 10-15% more damage than our average DD.
That being said, an alliance with 99 R/E DDs will kill 10-15% faster than average DDs. What the average DDs alliance takes 20 mins to kill, the pimped out 99s will take 17-18 mins to kill. Not a huge difference considering.
My point is, 99 R/E weapons have always been more trophy items than actual game changers. Honestly, I can only think of a few legitimate game changing items, and none of them are DD weapons (shields, instruments, stun staff comes to mind). So while I really do understand the concern of 99 R/E holders, they must also see the big picture and understand that their weapon never really changed their character as much as players made it out to.
This game is, and always was, about gearsets. Having competent gearsets, and using them appropriately makes a MUCH greater overall difference in gameplay than a singular weapon. So, if you have a 99 R/E then you obviously have the resources to have optimized your gearsets as well. The weapon is just the icing on the cake. So don't worry, it's not like the average Joe-Blow is going to be outdamaging you, regardless of what weapon they're using.