Password management (basic HTTP auth passwords, not with the wand) is crap - not possible to save passwords for entire directories - same page, different query string: "remeber password" option useless - password protected pages are not reloaded after crash (yes it's a feature but at least make it an option)
SSL certificate management is crap. - using an intranet with https and a fake certificate? wish you could tell Opera that certificate is OK? tough - "don't show this again" option doesn't work when using forms on inscure pages that send data scripts behind SSL
Installing new resets .ini files to defaults - spent hours customising your menus? you'll have to do it again, sorry
Changelogs are incomplete - eg: no notice that ctrl+space doesn't open your homepage in a new window; no notice that .ini files are incompatible; etc
Bug database is private - is this really necessary? why hide them if they're such an "open" browser?
Customer support is awful - no response to three emails about their directory of hotbar panels - no acknowledgement of bugs submitted - no acknowledgement or credit for patches sent
OK so it's still the best browser. But, sometimes, just arg.