Classic is naturally going to be slower, and drive RAM usage waaay waay up (since most or all of Mac OS 9 has to be loaded, emulated, along with whatever applications are running inside Classic). Classic has gotten better and better with each developer release of Mac OS X though. But I will be very happy when I no longer have to run it or boot into Mac OS 9.
As said above, the public beta is (most likely) in Debug mode. This does slow things down. And I really doubt that Carbon is still fully optimized yet. Cocoa apps seem (usually) pretty fast, both starting up and executing. But IE 5 and Sherlock both do seem to take much longer to activate. Since this is where most of the current development is going on (Cocoa is relatively stable at this point, while Carbon has been grafted into this environment at a relatively high speed), it's probably the least optimized. As many state, it's very important to file those bug reports and other general feedback to Apple!
(by the way: In the Grab Bag folder in Applications in Mac OS X, there's a CPU monitor. Through the CPU monitor you can also launch the Process Viewer or start a terminal session running 'top'.)
The IOKit is relatively new (it first showed up after DP3) but is a great system. I don't know if it's 100% complete yet or not, but I imagine it will still take some time for drivers to get ported over to it. Fortunately, IOKit is open sourced as part of Darwin, which should offer third party hardware and software makers opportunity to develop and test against it. Now that the Public Beta is out and IOKit's been around enough, I hope full support for it starts happening soon. This probably includes support for processor upgrades.
Finally, the Quartz\Quicktime\OpenGL graphics layer is probably not fully optimized yet either. Quartz behaviors started showing up in DP2 (and may not even have been in DP1), and weren't fully active until DP3. Quartz is a pretty advanced little piece of flesh, as Aqua fully demonstrates (live layer compositing, etc). Quartz is a vital component of Mac OS X for both Screen and Print purposes, so it's important that it too gets done right.
Mac OS 9 uses some shadowy tricks with its virtual memory system to speed up relaunch of applications, a hack that Mac OS X probably does NOT do. I haven't noticed a lot of splash screens in Mac OS X Carbon apps (hurray for bouncing dock icons btw!), which might add to the feeling that an app is taking a long time to load. GoLive and Photoshop in Mac OS 9 have a lot to go through when starting up, but the splash screen usually lets you know what's going on. The anti-modal ways of Mac OS X might discourage this tactic, but I'm not at all positive that's the case. Since the Mac OS X environment behaves differently that Mac OS 9, our mental mappings to visual cues that something's happening aren't rewired properly yet.
NeXTStep 2.0 seemed to SCREAM on a 68040. I'd be shocked if the GM of Mac OS X doesn't follow suit.