If you are like me, you have a certain way that you organize your luggage. In other words, I know that my Eagle Creek Pack-It Garment Folder will go on the left side of my luggage and then a couple of packing cubes will fit flat on the right side. Once I've got everything inside the packing cubes, tossing them into the suitcase takes just a few minutes because I already know where everything will fit. When I get to a hotel, I just place the packing cubes into drawers. (I am male, by the way. My wife also uses eBags, but organizes differently than I. Her eBags have a cute leopard pattern.)
Like you, I've been using eBags packing cubes for quite a few years, but have recently substituted a few compression packing cubes to save space. I have 2 different brands of compression cubes:
1. an Eagle Creek compression cube that I've owned and used for several years
2. a pack all compression cube that I purchased on Amazon this year (because I couldn't find another Eagle Creek like the one I already own). This has dual zippers and works similarly to the Eagle Creek compression cube. So far I am pleased with it and will likely purchase another. Link:
How did I select which compression cube to buy? I measured the length and width of my eBag packing cubes. I wanted compression cubes that were about the same dimensions when zipped up because I wanted to place them into my luggage in exactly the same spot as the old eBags. Yes, they do save space.
Shirts and long pants go into the Eagle Creek Garment folder. I have no problem with wrinkling. I love that garment folder. (I had to buy one for my wife after she saw how great these are. Hers has a cute zebra pattern.)
Things such as T-shirts, undies, socks, swimsuits, sleepwear, and exercise gear usually go into the packing cubes. The only item here where I care about wrinkling is the T-shirts, and only really in the summer months. (In the winter, T-shirts are underneath, so wrinkles don't matter much.) If you pack T-shirts flat, yes, there will be more wrinkling in the compression cubes, but I think it's an acceptable trade-off for the space you save. If you are a roller, I don't think you will notice as much change.