How do people keep track of all these modifiers? With chits or other such markers?
I use a set of Alea magnets. They work pretty darn well, now that they're the neodymium sort and don't interfere with one another nearly as much.
Also--and this is more rhetorical--if everybody has special powers, then they really aren't so special.
I hear this a lot, and I think it's a pretty hollow catchphrase. It sounds good, so people say it a lot, but it doesn't make much sense. Basically, you're conflating definitions of "special."
2. Combats aren't scary for the players
With all the healing surges, cleric's minor actions to heal, and finally three saving throws when a PC drops, most combats just don't seem intense as they should be for the players. This sort of fits in with this thread:
http://www.enworld.org/forum/general-rpg-discussion/247429-d-d-4th-edition-creatures-not-scary.html
Monsters just don't seem to do as much damage as they should.
In 3.5e, players would think along the terms of CR--that was easily solved with tossing in higher CR monsters. But in 4e, there's just so many second chances that even more powerful monsters just don't scare the PCs like they should.
What can be done?
Hm. All I can say is that I haven't found this very much. My players go into many fights thinking "Oh, we're screwed" within the first few rounds. That's when the tactics kick in, the abilities kick in, and ... it never becomes easy, but it is made to be manageable.
One of the things I've noticed in my group is that an extra leader makes a gigantic difference. Do you have a cleric and a warlord in your group, maybe?
3. Combat Grind
This has been covered in other threads, so I won't belabor it here. One solution is to use more minions, but that makes combat even less scary. I'm sort of at an impasse with this, and haven't found a desirable solution.
There's two ways to approach this. They are, of course, directly contradictory.
(1) Grind isn't inevitable. It's a direct result of mediocre tactics. Improved tactics will minimize grind. If the whole party isn't working together to set up their buddies, combat will last much longer than it should.
or
(2) Grind is almost inevitable, given the system. In this case, I think the best thing you can do is reduce all enemy defenses by 2 and increase their damage by 1/2 their level whenever you see a combat grinding. This won't block poor rolls, but it will help everyone land their attacks a lot better.
Regardless, I think a great way to minimize grind is (as mearls said) to scale back on elites and solos. I think it's one reason Pyramid of Shadows can feel so grindy at times.
-O