Are encounters naturally weighted against players and how do we 'fix' it?
Yes, Descent (both First and Second Editions) is weighted against the Heroes.

Descent is a board game designed to play like a Role-Playing Game (RPG), so it includes the classic thematic elements of heroic player-characters striving against an unknown evil entity seeking to do Evil Things with the aid of his endless ranks of minions. 

In most RPGs, the monsters will frequently have abilities or stats that the players can only achieve at much later levels, or sometimes never obtain. This is designed to force the players to adapt to overcome the situation, to use teamwork, tactics, and preparation to collectively achieve what no individual could otherwise.

It sounds like what happened to your party was that the Overlord caught you in a standard RPG pitfall: The party became too narrowly focused. Maybe there were no ranged attackers, in favor of heavy-hitting melee? Maybe there was nobody with high Might because everyone focused on Awareness? There's all kinds of ways to leave 'gaps' in your group's abilities, but the important part for you as a heroic player is to learn to overcome them, either by conquering them when they arise or protecting against them ever becoming an issue.

One of the typical ploys in Role Playing is to present the players with a 'teaser' of something evil coming up, just enough so that they can possibly plan and prepare to survive it: a corpse found at the entrance to a dark cave covered in massive spiderwebs (indicating serious spiders inside), or a hallway covered in scorch marks ending in a door burned down to the hinges (indicating a fiery foe awaiting invaders). The problem is, if the players do not respond to this teaser or are unable to adapt to the situation, The Bad Guy is going to beat them. Badly. Defeat happens.

The important thing to take away from a defeat like that (either as a character who somehow survives or at least as a player preparing for their next character) is to look at what happened, look at your available options (skills/feats/abilities, equipment, etc) and try to work out a way to defeat the tactic the next time you see it happening. Perhaps some form of ranged/reach attack so you can still remove threats while immobilized; perhaps a plan to focus-fire on anything that appears behind your team to make sure it can't harass you; or perhaps just changing your plans for who-moves-where to better provide protection for the whole team.

Yes, Descent is weighted against the Heroes. That's the whole difficulty of balancing any RPG or Role-Play-like game: finding the point where the Heroes *can* win, but so can the Overlord, and the difference is teamwork, tactics, and creativity.