I install everything but the Standing Stones modules. SkyRe leaves the Guardian Stones unchanged and I prefer to have them increase damage rather than the speed of leveling. I also prefer the vanilla Lord Stone values (a lot of my characters wear only Light Armor so the vanilla 50 AR can come in handy for them).
I make a few changes to the Uncapper. I change the amount that certain skills contribute toward my character level-ups (I change this to anywhere between 0.5 and 0.1). I also change the speed at which certain skills level up (some faster, most slower). I change these values when I start a new game to suit the particular character I'm playing. Lastly, I give my characters 3 or 4 perks at level 2, to simulate a character's prior experience. I see this as a kind of home-made "class."
Other than that, I "tweak" SkyRe by using using other mods like Immersive Creatures, Deadly Dragons, Immersive Armor and Improved Potion Animation (to cut down on my temptation to spam potions). I don't usually install Immersive Weapons (as great as that mod is) because SkyRe already adds most of them into the game.