That's because the Win98 code is that much simpler. It has less to do with speed and more to do with complexity.
Your phone is doing all sorts of weird shit behind your back as you poke about. Stuff that it's not supposed to be doing if app-makers were actually respectful of their users...
On that note, why does that crap take so long on smartphones anyway?
One tweak that made my G2 feel much more responsive is simply turning down the UI animation length in Dev Settings.
That's not to say that app developers don't love their non-native webview apps crammed to the brim with ads, though...
UI animations have a lot to do with it, but I'm more referring to UI jank over simple stuff like 'enumerating a list of sharing targets' or 'swiping to the next page of the launchboard' when the phone is otherwise idle. Or, my favorites: the multi-second pause from unlocking my phone during a phone/skype call, or the taking of an actual eternity just to answer said fucking Skype call, of which half the time the call has already hung up once my phone is finally responding...
That's why I switched to windows phone. It's a whole new experience. I can actually answer my phone without the obligatory wait for catch up before I can swipe to answer.
Had a client who later wanted me to do add all sorts of nasty things to an Android app template that I had made for him: Locking out primary navigation buttons, partially replacing the home app, spying on the user, and the capability to send out very expensive SMS texts and auto dial long distance phone calls. Unfortunately I was unavailable to do the addons he wanted, despite him asking repeatedly over the next 18 months. Never trust an Android app...
I think a big part of it is simply loading in resources and the like. Smartphones try to keep a _lot_ of apps in memory, so there's a lot of switching around.
Another thing is that Windows would put certain native widgets (like file selection) on a higher priority than other program code. Android, at least, tries to put as much stuff in userspace as possible, so you might be experiencing the reality if everything run at the same priority.
I miss the shitty machinery of win9x days[1]. The weird part is that I was deep into CGI, and compositors made so much sense to allow for all kind of graphical operations; yet.. I miss the refreshed icons, blinking cursor .. as if I was one to one with that simple machine.
That's very subjective, I'm in a minimalist passeist phase.