You know, it's just one trade-off and it might not be much worse than linking C++ dynamically... Or Jitting Java byte code.
I have owned an Agenda VR3 and a Zaurus. I can tell you that there are many ways to wast CPU cycles and that in any case it takes effort to avoid them. The Agenda guys spent a lot of time trying to optimize the binaries and resolve issues caused by C++. They might have had an easier time coding in Python and avoiding C++. Or not. It's a complex issue, so it's hard to say even now after the dust has settled.
I don't think there is any silver bullet nor that Javascript, Dalvik or C++ are bad per se. What matters is the effort that the makers put into integrating the software and the hardware, testing, optimizing etc.
The Pre uses the V8 Javascript engine and it might be more efficient to jit a few tens of lines of Javascript than to link a C++ binary with all kinds of libraries (say stdc++, qt, X11 etc.).
Also, I remember that programming in GFA Basic and running the programs on my 8MHz Atari was quite fast actually. So why would it be such a mistake on Palm's part to use Javascript on a machine that is about 500 times faster (the fastest instruction took 4 clock cycles on the 68k)?
I think the Pre is really interesting as almost everything in it is Open Source (V8, Webkit, Linux etc.), based on standards (HTML, Javascript). Also people seem to be able to compare it with the iPhone without laughing so it must be a rather good integration of hardware and software too...
Anyway just my 2 cents and an occasion to fondly remember the gadgets of my youth ;-)