Really wish I had this advice BEFORE I ran the encounter. That sounds like so much more fun.
Ok, now that I've perhaps given out more than my fair share of the lecturing and criticizing

, let me focus on some more heartfelt advice. I'd say the best single piece of advice to keep in mind for future encounters is: Focus on variety.
Variety of Enemy Roles
Minions are one of the great things 4E has added, but they are only part of it. An encounter filled with a bunch of copies of the same creature has two issues: One, it isn't going to be as exciting as a more varied encounter, and two, it has much more risk of the group being especially weak against those specific enemies. (Or especially well-suited to defeating them, which can be just as frustrating.)
The DMG has some good advice on this, and a bunch of different suggestions, but the core of the advice is to have a bunch of different roles represented. Some monsters that get in the party's face and distract them, others that lead from behind the scenes, others that sneak around and try to shank the party's wizard.
Variety of Enemy Power Levels
An alternative to that, for having an interesting fight, is to have a variety of power level amongst the enemies. In the example encounter I gave, we have three levels of power:
The Wraith, who is an obvious leader figure - not in the mechanical sense of providing any bonuses to his allies, but in the sense of being a central figure that will focus the combat and constantly have the party's attention.
Next we have the normal Skeletons - when describing the scene, I'd probably have these mentioned as looking like the corpses of soldiers, with still intact armor and weaponry, clearly establishing them as more of a threat than the lesser skeletons falling apart around them. What they do is provide something of a baseline of power for the PCs to compare against - any given PC might be able to go one on one with these guys and take it, but they don't have the luxury in this large, sprawling battle. More than that, it spooks the PCs to see these tough sturdy skeletons next to the little guys - they might get worried that, if the combat goes long enough, more of the tough guys will show up. That keeps them guessing, and makes it harder for them to just assume things will go their way.
Finally, we have the minions - cannon fodder, but in 4E, cannon fodder that still presents a threat. Having them come in waves (rather than throwing 20 or 30 at the group right away) actually works in their favor - the PCs are likely to burn some of their biggest area effects early, and this way you don't have all the minions wiped out right at the start of combat. In the end, they aren't the focus, but they also can't be ignored - a single one isn't dangerous, but letting them build up out of control is a recipe for disaster.
Variety of Scenery
Finally, having interesting scenery and terrain in an encounter is a very valuable tool. This one you had a solid hold of in your original plan - while the fight starts in a clearing between two buildings, the buildings were available to be part of the encounter, and a well was present for encouragement of forced movement abilities.
Unfortunately, one of the things I've noticed about 4E is that while it presents a great number of opportunities, it can take a while for players to get into the mindset of taking advantage of them. This, really, seemed to be the main point of your original post - that the players didn't even consider moving into the building at all.
What can you do to fix this? Well, in part, simply run more encounters with similar opportunities. Some of this
is just a matter of getting used to the opportunities in the new edition, and the more the players experience it, the more comfortable they will feel doing so.
Additionally, trying to make such options feel more accessible. I mentioned before that many players might be afraid to dive into an unexplored area in the midst of combat. For some, this is from years of playing with tricksy DMs who have traps and nastiness hidden around every corner. For others, simply out of fear of the unknown - even if the risk is small, if it could tip the balance of a fight, it might not be worth taking... and thus, by the time they are willing to risk it, the fight might be already lost.
How can you get around this? More information always helps - do what you can to ease the player's fears. Maybe the door is swinging open and they can see the way is clear - maybe there
are enemies inside, but in small enough numbers that they can be easily dispatched, thus drawing the PCs in from the beginning, and rewarding them for going that route.
Sometimes there won't be anything you can do to get PCs to make use of the environment the way you want them to - but that's ok. Not every fight needs to be fought the way you planned it, and adapting on the fly can sometimes make it as exciting for you as it is for the players.
In the scenario I gave, I would probably encourage the PCs to move into the house by making it look like a good defensive spot against the hordes of undead - or perhaps lure them in there by having the Wraith use it to keep safe, darting in and out of the walls, thus forcing them to chase it down. Once inside, skeletons start forcing their ways inside from all directions, through the doors, the windows, the chimney... if you can get a classic horror movie feel in there, then go for it!
But it doesn't need to be forced if the players do something unexpected. Maybe they retreat away from the building, thus forcing the Wraith to come after them - and while this lets more skeletons close in around them, it also might let them make better use of their area effects and explosive spells. Or maybe they retreat to the center of the area, fighting back to back so they can't be easily flanked, and find a way to set the houses ablaze to force the Wraith to come out into the open.
So I guess that is two important bits of advice: Make good use of variety to keep encounters interesting, and be prepared for the players to react unexpectedly... which keeps things interesting for you.
