I would like to see more difficult bosses in the game, and longer dungeons to go with them.
I don't want to spoil anything by naming stats, but having run through the entire game except for the cazaul shrine, I haven't found the boss fights all the challenging. I'm used to saving right before bosses because even when you are "at the right level" the boss fights are still challenging, but I have noticed that the bosses in AT never really represent a big increase in difficulty over the mobs surrounding them.
You can also tend to get to the boss without facing too much resistance.
For example examine the Gargoyle Caves. Sure you face a fair number of Gargoyles, but once you make it to the final rooms, you don't even need to explore them all to get to the boss. You have 3 trainers/master in the first room that can be dodges if fast, 2 unavoidable in the throne room, and then 3 more you can dodge.
You could theoretically get in and out of the trainer/master room having only faced 1 trainer and 1 master before fighting the boss.
I think bosses should be stronger to make you work a little harder to clear the dungeon/finish the quest, and the dungeon to get to the bosses should be a bit more elaborate. This will help add play-time to the game and decrease the difference in experience between grinding for items and normal game play.
The same goes for some of the major quest NPC battles. I have almost all of them to be child's play after dealing with the surrounding mobs, especially the later ones.
I also like your idea of having more monsters that you can't avoid on the way to the boss, besides having the actual boss be stronger.
One way to make them stronger is to give them character conditions.
A good example is the Auleth, which get +1 HP on hit. It doesn't help them much if we can hit them really hard, but its a good basic idea. If the boss can get a critical hit, that also makes them pretty strong, and being able to cause a condition like Fatigue or Chaotic Grip could help too.
Some other suggestions for a boss, to give them one (or some, but not all) of the following:
Strong Life Steal: +5 HP on hit (similar to ROL but guarantee 5 each hit)
Boss cleave: +3 AP on hit (instead of on kill since its just fighting one of us)
Super Regeneration: +5 HP each turn Magic Damage Resistance Force Shield: reduces the damage of our attacks by 25-50%
Critical Cancel: if struck by a critical hit, has a 50% chance of reducing the Critical Multiplier to 0.
But if the bosses get tougher, the reward (XP, gold, items) for killing them should also get better.
A few people had previously mentioned it would be more challenging to fight someone as strong as your own character, so with that in mind, here's a few more ideas.
Weaponeer - able to copy the stats of whatever weapon the player has equipped (stacks onto monster's existing stats).
Knockoff - copies all equipped stats from player (stacks onto monster's existing stats).
Skilled copycat - copies all combat based skills the player has.
Would not copy non-combat skills (Quick Learner, Magic Finder, Treasure Hunter, etc.)
Would also not copy skills that take effect on enemy's death (Corpse Eater, Cleave).