Earlier quoted context omitted.
It's because of drivers and PnP and especially USB. When you load Win3.1, WinNT4 and lower, drivers load without scanning for hardware presence. It's just a disk to memory copy. In Win95, the first PnP OS, it scans for PnP hardware at every boot. That's slow. To prove my point, you could try loading some of the USB drivers for DOS or one of the ISA PnP configuration utilities (such as ICU - Intel Configuration Utilit…
Besides the boot (which windows 3 didn't even do so I don't see why we are comparing it), from clicking on the start menu the 1st time after boot, to the start menu actually appearing on screen it would take 1-2 minutes to populate on windows 95, while on windows 3 on the same machine there would be no such issue.
You are probably thinking of Win98 menu where they added IE.