1) I decided that each time the PCs take an extended rest in the Pyramid, they would be visited by dreams of the past, slowly unfolding the tale of Karavakos, the primary antagonist of the adventure.
2) I plotted out a bit more interaction between the various groups in the Pyramid. The adventure itself has some advice on this, though I largely invented some of my own ideas - I had one area (the Library) initially sealed off by the Arboreans (plant people). This was both to let the PCs have a sense of build-up before reaching the Library (which has both valuable information and the 'boss battle' of the first floor), and also to add the feel of a place with constant powerplays and manuevering between the various beings trapped inside. (In this case, the Arboreans were afraid of the creatures that had moved into the Library.) In order for the PCs to get into the Library, they needed to either defeat the Arboreans and their Plant God, or find a way to bargain with them instead.
3) The adventure implies that the Libary contains all the knowledge of all the creatures trapped within the Pyramid. I decided to expand on this a bit - first off, by deciding that this knowledge is at the same time lost to the outside world (and so any imprisoned within are forgotten by those who knew them, vanish from records, and so forth), which added a sense of mystery to the quests I initially sent them on to find the Pyramid. I then also created some handouts with summaries of various 'novels' they can find in the Library - some of which describe the PCs themselves, some of which describe the most distinct monsters they will encounter within the Pyramid. I think this will help personalize some of the encounters, even before they stumble into the different areas that await them. It also lets me share some background knowledge that they might miss if they simply hack their way through everything in their path.
4) Pyramid of Shadows has one solid NPC already - Vyrellis, the NPC Spirit of an Eladrin Princess / Artifact that the group encounters early on. I plotted out a bit on what information she will reveal as the PCs gain her trust, and feel that she will be a key NPC to keep their interest throughout the adventure.
5) To my surprise, I found a second NPC becoming important in the first session - a Satyr who had allied with the Arboreans and 'surrendered' to the PCs. He managed to convince them the Arboreans had magically controlled him (not actually true) - and then helped them fight to victory against those same Arboreans. Now I need to decide what to do with him - the party seems to like him, and he acted quite heroically in the battles, but I don't really want him to just become a sidekick.
I'm tentatively thinking of having him become more and more boastful as they encounter other groups in the Pyramid (as well as when I introduce the PCs who missed the first session.) The adventure suggests he eventually will try to steal from them and sneak away in the night, to join some other group - once they get fed up enough with him, that is what I plan to do so, with a catch... I plan to have him steal the orb with the essence of Vyrellis in it, which should give them pretty solid motivation to track him down right away. What group he will join up with I haven't yet figured out - but again, I see it as a chance for more interaction between the forces within the Pyramid.
6) Finally, I've added one extremely complex skill challenge near the end of the adventure, since it is only has a few of them. In one of the undead halls on the third level, once the party defeats the undead within, I plan to have an event where the necromantic power in the room begins to build out of control (since one of the undead in the room had been keeping it in check.) There are four statues in the room, a Death Knight, a Vampire, a Mummy and a Lich - I decided they are actually ancient undead petrified and imprisoned when they were drawn into the Pyramid, and whose power is being harvested by the Necromancer in charge of the undead area. Now, that power is building up into a massive explosion. The PCs will need to either break out of the room and flee the explosion of dark energy, break the statues (which releases the imprisoned creatures, who they will then have to defeat), or find a way to purify the statues. I have some background for the four statues (who are all actually from the time of the tiefling empire), and there will be a ghost wyvern floating around to help the PCs out with cryptic advice - like I said, a very complicated scenario, with several ways to overcome it, some of them with greater rewards than others.
It is pretty much an entirely isolated plot point from the rest of the adventure, but provides for a good stand alone challenge for the group. (And I find Skill Challenges with a timer on them are best suited to making for a really dramatic scene.)
Conclusion
So, those are some of the various plans I have for making the adventure seem like a bit more than just a standard dungeon crawl. The group I am running for is probably going to just hack through most enemies anyway, but I'm trying to get a bit of investment for them in the story of the bad guy and some of the major foes they will fight. That was the problem I had with Thunderspire Mountain, which a friend just finished running - we never really cared about any of the enemies we were fighting, even the final villain. A dungeon crawl can still be exciting, but you need to have some amount of investment, or it is just rolling dice and collecting loot.
