Rebuild Layers was a complete kludge to get around the deficiencies of layers. For a start, it was pretty random itself as to how it repositioned clips. I used it a lot in 8.5.3, but I think in X2, with Take Lanes, the whole problem goes away.
Yes, you'll have to change your way of working slightly, but in my opinion, we'll be better off.
I know people told me similar things about X1, and I basically said, "no way, don't tell me to change my process, I'm sticking with 8.5.3, then", so I know this is a very subjective thing. You're certainly within your rights to call this a deal-breaker and not upgrade.