Well I did some more testing and I have to take some of my words back. Running Starstruck (TBL) demo they are all equally fast EUAE-wip4, EUAE-080815 and WinUAE 1.5.1 and this demo is watchable. So it's not a speed issue. Now I suspect that certain speed issues are related to file IO operations. I'm using a directory on the host system as Amiga partition on both systems/emulators. So it looks like they improved that part in WinUAE 1.5.0+.
It's especially the start menu in AmiKit which is very slow. And f.ex. opening drawers is slow too. (EUAE and WinUAE versions before 1.5.0. On WinUAE 1.5.0 and 1.5.1 AmiKit is much more faster and more usable.) I tried to edit one config file of AmiKit to get rid of icons in the start menu. Now the taskbar is huge vertically and I can't get it back to original size trying to put back everything I changed (I think) in that config file I edited.
Unfortunately the latest Gparted for Ubuntu doesn't support creating AFFS or SFS partitions so I could test if AmiKit would work faster using native partitions. I tried to install the latest Gparted (0.3.8) but I couldn't make it to work. (And I don't know if it yet supports AFFS and SFS anyway.)
(My system is: 1500 MHz AMD Athlon, single core, 32 bit, Nvidia FX5600 ultra)
One offtopic note: Testing old Aegis Sonix 2.0 on all versions of UAE. WinUAE have had always the worst playback losing many notes and it played never good (testing with different possible emulator settings) (I don't know if it works better with much faster CPU's). EUAE on Linux (x86) is a little bit better but it's still far away from perfect playback. But strangely the same EUAE on AmigaOne and AOS4 it plays almost 100% perfectly but not fully but very close. So is it because PPC CPU's have good timers or is it because Amiga kernel is faster or pure luck or something else ?