When I ran it, my group ended up heading into the Arborean's area right away, and the encounter with their leader and the plant god went over really, really well. Having this primal force of nature uprooting trees from the ground and hurling stone plinths at the invaders - the entire interaction between the scenery and the combatants really made that encounter.
The most intense fight was with the white dragon, who I had given a name and backstory and had the PCs learn about earlier in the temple... but I also modified the encounter a bit, adding in a bunch of 'ice bat' minions and other support. (Partly to just make it more tougher in general, partly to compensate for the party size being 6-7 PCs). Plus, of course, awesome map, and I made the dragon huge (with no other mechanical changes) just to use the excellent Huge White Dragon mini.
There are a lot of good encounters in there... the Headless Corpse, any of the Karavakos fights (especially the final one)... I know the party was appropriately squicked out by venturing in the Heart of Madness and fighting the aberrations in there.
I do like the Palace of Bones fight, and it does have a very nice map, but I'd recommend being slightly careful if you use it. It was probably the worst fight I ran for my group, just because the grasping bones hazard really constantly shut down melee characters in a way that was frustrating, rather than challenging. Weaken or adjust that, though, and it could be a good fight.
I'd say finding one fight to really capture the place will be hard - the best part of the adventure is having so many different environs all trapped within the place - but I do think the Arborean area can work well. Have the PCs explore the outer areas (removing the enemies or making them all easy to defeat), maybe work in a skill challenge or other event as they encounter this rampant growth within the Pyramid... and eventually they reach the Arborean's Temple at the end, and can defeat the druid, his pet bear, and his plant 'god'.
Then have the spirit of Karavakos appear and mockingly thank them for removing a threat to him from the Pyramid, and cast them back out, or similar... which should help things make sense overall, rather than just having them show up, get in a fight, and get out.
If you are willing to spend a little more time there, you could expand on this a bit, and just have the group fight all the 'boss monsters' in the Temple. (Perhaps on behalf of Karavakos). He might send them to fetch some magical trinket from the Arboreans, the Dragon, the Bandit Warlord, and maybe defeat his other selves along the way. All the other enemies they encounter can either be made into minions - or better yet, have open warfare be in the midst of erupting between the different fashions, so that they are constantly stumbling into fights where different groups are cutting each other down, or entering a room where everyone is already dead or dying, etc. (Maybe even let the PCs be the ones turning those groups against each other, depending on how hands on they are).
That would let the PCs only have to deal with less than half a dozen fights (potentially doable in 1-2 sessions), while still getting a tour of the Pyramid. And eventually they reach Karavakos and can either help him open the way out, or fight him and escape on their own (if you decide to keep Vyrellis in the adventure.)
