I play the game as is, with very few exceptions.
I tend not to run skill challenges as written, unless I really feel that they're appropriate for the scene. Instead I just adjudicate like I used to, with players needing to accomplish whatever "makes sense" at the moment. Of course, I have adjusted how I do this as a result of learning about skill challenges- I tend to more heavily favor multiple check skill based encounters and I tend to put more thought into making sure that more characters can be involved at a time. I do use skill challenges for matters that have obvious degrees of success, or which can easily be conceived of in terms of each individual effort contributing to the overall "amount" of success. Use drops of water in a bucket as an example- it doesn't matter how the drops got in there, it just matters how many.
I don't give out XP based on the XP schedule. Instead I just handle level ups like I did in 3e- whenever it feels right. I do use XP for determining combat difficulty, and feel this works reasonably well.
I think minions work incredibly well when there are just a handful of them accompanying other more important monsters. I do not use encounters of nothing but minions. I often use minions in waves as part of reinforcements, as this protects them from single round obliteration. Sometimes I use what we might call respawning minions- skeletons that raise from the dead, for example. As I do not give out XP for monsters killed, this causes no particular problems.
I think that in modules WotC foolishing holds themselves to a strict "add up the monsters" style of determining challenge level and XP. WotC regularly issues realistic but intentionally poor tactics for their monsters, or combines monster synergies in highly effective ways, particularly in combination with terrain that is not officially a hazard and therefore not worth XP. The first results in a challenge of lower difficulty than assigned, and the latter in a challenge of higher difficulty. To give an example of what I mean, imagine a fight with a monster that can push targets it hits two spaces. If you fight this monster in a featureless plane, its worth 1000 xp. If you fight it in a room with a trap that sprays acid, then maybe the encounter is worth 1,200 xp, and you'll see some neat effects when the monster throws a PC into the trap. If you fight this monster in a room with a giant 40 foot deep hole in the floor that isn't a trap, just a feature of the room, the encounter is worth 1000 xp again, even though it may very well be far, far more deadly than the room with the acid. I try to keep careful watch on these things when I run published modules.
There's probably more, but that's what I can think up on the spot.