Person asking question, I would definitely say it's almost certainly playstyle. Exactly what, I couldn't say, but I very regularly do basically what you're doing in regards to order (though I tend to hit the maze before OF) and come out fine. I'd kinda' disagree that the alt-dungeons are particularly more difficult than the mainline ones (though the main maze is significantly less of a pain in the arse to navigate), and haven't bothered skipping them in a long, long time. I do alt-maze at 11 or 12, I do main maze at 11 or 12 -- same for OF, if I've already found waterbreathing kit (because I go straight into the lake). Swinging by to at least off the bosses on all the T1s is a pretty good idea, though. I often outright skip the sandworm lair nowadays... I love the heart, but half the time I can't be arsed to navigate the thing.
Wrathroot... if you've got a decent heal (regen or otherwise) the freeze is scary but frankly painless -- the CD on it is too long to be a genuine threat in the face of semi-decent (say, 150+ on regen, ~100+ on heal providing the CD is <10, stuff like that) inscriptions. Getting into melee can help there, if you're a melee class, since that can often screw with the boss's AI a little (i.e. they'll just whack you instead of doing something useful).
In regards to the snow giants, you want to take advantage of the terrain and make sure you let boulder throwers come to you -- they're the only genuine threat in that zone, imo, and if you get yourself in an open space with three or four of them, they will wreck you into the ground. If you can keep it one-on-one (and hopefully stun/daze/etc. that gorram freakishly OP boulder throwing talent into non-use) they usually fold fairly easily. Also, protip on confusion: If you're confused and you want to melee something, use the attack talent. I've got it hotkeyed to / on the numpad. If you try to move into the enemy to attack, it will often move you instead of taking a swing. Trying to actually use the attack talent does not have that problem.
Shadowblades and assassin lord sounds like you might be having problems with accuracy. Usually so long as you can hit them (and, preferably, have no more than one beside you at a time) they fold fairly easily. Push comes to shove, just kite until you can heal up. Also, that attack talent again. Or just melee talents in general -- so long as there's just one critter beside you, it'll autoswing at it even if you can't, technically, see the thing.
... all that said, I usually pay... basically absolutely no attention to my saves. Sometimes they're good, sometimes they're not. I just don't really notice or care. Most status effects that aren't straight up damage have ways to react that help mitigate their effects, so you can often push through daikara with no confusion resists/low msave, and so forth, just by knowing how to react while confused to keep yourself from keeling over. Same for a lot of stuff, really.