What advantages are gained to the system if you make the change?
* Difference from high vs. low level - how does this improve the game? I would argue it may even deter from it.
* Enhances Rogues ability to win initiative, which is a key advantage for them. - this is a plus.
* Provides a significant advantage to all the monsters who have "all good saves" such as Demons, Devils, and Dragons...I'm sure there are others - I think this might be an unintended disadvantage
* A little easier to track than keeping initiative separately
* What bonuses would stack with Ref save (enhancement bonusest to Dex, resistance bonuses, Great Reflexes Feat, etc.)? - Is this a potential balance issue, allowing people to over-capitalize on this advantage?
The other question to ask yourself is, "Is there any other way to accomodate the benefits, without the disadvantages?" (ie, what about instituting a generic +1/x lvls to initiative for PC's?)
Solely playing devil's advocate here, I think it's an interesting idea.