Question: What is the single most important difference between Gun'drak and Halls of Lightning?
Answer: Order of boss difficulty.
There are a couple forces competing with each other in instance design. One is the idea of the last boss being the hardest, the coolest, the badass of the place who makes all previous bosses seem trivial. This is the coolness force. The other is the playability force, it asks "if you start this instance, can you finish it?" This force obviously works towards short instances so people don't have to leave halfway in (this was an area where BRD was pretty bad). It also encourages instances that only save you to them once you've demonstrated that you have a good chance of completing them.
Gun'drak is usually done with the snake boss first. This one is fairly difficult. This is a good thing. If you're saved to Gun'drak, you either ran it backwards or your group is good enough to beat it.
HoL is the total opposite. The first boss is trivial. If you can beat the first boss, you just might wipe on the second. The third is easy. Beating all three of those does not mean your group can do Loken. He's not a gear check or a composition check or a healing check. All he tests is whether or not your group members are capable of moving at the right times in the right direction. It's actually simple, but it's a skill that is rarely tested and is not tested in HoL until you're already saved.
Making the last boss the hardest sounds cool, but in terms of playability, it's terrible. To make it even worse, the last bosses drop epics and daily quest items, so to many people they're the only bosses that matter. To get to the end, the goal, and then get held back by a fail group, which you had no chance before to see if it was full of fail, that is not fun or challenging, that is just frustrating.
Trash doesn't help either. After too many wipes, even if you've not called off the run, the trash is back. Now you have to redo the entire instance, as if you'd never started, except with no badges along the way and with a group that you already know is bad.
TL;DR: For the sake of player sanity, put skill checks at the START of instances, not the end.