1. Desktop "Compositor" and "Quick Comp". Compositor is a watered down Action that actually takes longer because you have to up the resolution to see anything worthwhile. Using it is like staring through a time warp. I saw Mike Semour fire it up once in an FXPHD course, but I'm willing to guess it was for novelty alone. There is absolutely no reason to keep this archaic alternate way to skin a cat in the software. Quick Comp sucks as well because it's just a Logic Op Blend, but has only like two features. I suppose if you are afraid of Batch and can't be bothered to divide your fills, then this guy is your lazy-assed bread and butter.
2. Desktop Logic Op. I've got a bit of an axe to grind with the Desktop buttons in general. Prior to Batch they made sense, but now that all those features and many more are available in Batch, and you can preview your results, animate your results and everything else, the use for desktop Logic Opping is mininal and could probably be grouped with Quick Comp and others.
3. The lack of a color warper on the desktop. Yeah, I know it's inside the CC node, but that is a huge pain, mostly because any CW setup you save off the desktop goes into your CC folder and you have to go hunting for it, should you load said setup into a CW in the MK or Batch.
4. The Keyer. Seriously, I hate it. Use the nodes in Batch. As a bit of an aside, why the hell does the MK name the output "keyresult" even after you've named the setup. That's just silly. Fuck both these nodes. Use Batch.
5. Action's particle system. I've just finished a job where I used particles reasonably heavily. Said job also got me to be an expert on faking particles, since using the system in Flame is convoluted. I'll write another post about why I think it's so important that this feature get updated, otherwise this bullet point is going to be seven paragraphs.