Let me just put it this way.
I'm not 100% sure if the problem is related to the controllers or the bluetooth module within the PS3. I hear reports of less dropouts with the Dual Shock 3 and I heard less drop outs with the newer PS3 models (like the 40GB especially and somewhat with the 80GB, since they do use a different frequency). But overall, there is a weird bluetooth problem with the modules Sony chose, and it doesn't seem to be fixable even by firmware (it's a hardware issue, kind of like you can't make software fix bad hardware saying). I've worked with bluetooth modules myself when building some electronics, and there were some I came across that have issues staying connected with each other.
Right now, we gotta live with it. I'm personally thinking they'll just be using a new bluetooth in newer consoles which won't have the problem (and which will work better with the DS3).
If it was something that could easily be fixed, we'd probably have it by now (before Firmware update 1.5, PS2 games use to appear very jaggy on PS3 due to scaling issues. The firmware fixed that issue).