Doctor M said:
Love the blooming fixes.

I've been avoiding this thread because I didn't get to see this until a few days ago.

I also like all the ideas in the first post.

My suggestions:

In the jungle chase the tree cutting machine: When it blows up, it's almost unclear what happened. Unfortunately this is one case where MORE footage is needed. I was actually asked by one person what happened and where that spinning blade came from.

In the jungle car chase, Spalko shoots at Indy but shoots her own men: It's very fast, and difficult to see happen. Enhanced gun fire, hits, yells, and muzzle flashes might make the scene work better.

Again the jungle chase, at one point Mutt jumps from his original vehicle to the one with Spalko. It's done in a long shot with lots of CG vegetation in front of it obscuring the shot. (I had to back up while watching to figure out how Mutt changed vehicles.)

Ants hill: Cut the ands forming a tower trying to reach Spalko. It looks REALLY bad.

CG work: Marion has a stupid smirk on her face for 90% of the movie. What the HECK was that about? Was she just happy to be acting again?

Area51: When Indy breaks through the wall of boxes, it's all box material. It LOOKS like he drove through a single thin wall of empty crates. More debris, packing material, and odd artifacts need to be added.

Definitely cut 'Trust me'. It was a good line, but she didn't deliver it well.

I definitely agree with everything you said here. Laser, where art thou?