Regarding skills: if you look at the highest teir of your starting skills, it shows the options you have once you buy that tier to morph it into an advanced form. It appears to have two separate choices for each of the skills, for instance, my soldier can morph his ammo skills into either one that applies for the entire team, or an improved verson. Or he can morph his class skill into either the Commando or um...something else, each providing different bonuses. One seemed more geared towards melee, the other towards precision shooting.
So I think alot of the accusations towards a dumbed down skill system is coming from people who have not noticed this rather large spread in truth. Also, each of my two companions has a skill I cannot place ranks into until I raise their "trust" in me.
Equipment:There is a helmet toggle, there's an entire armor/clothing customization locker where you can change between various patterns, appearances, cammo and colors for your armor. Right now I only have the collectors and the basic N7 armor as a choice, but you will receive more as the game progresses. There's no more armor classes however, will see how this pans out.
Regarding the gear, the "loadout" you choose at the start of the mission appears to be what you're stuck with for most of the mission, although there is the capability to pick up weapons. Only done two missions so far however, so no idea how that will progress.
Missions: These are very interestingly done. It actually reminds me quite a bit of DDO in a way, each mission is much like an instance, and at the end you see a "results" screen, where it's a report to the Illusive Man. It shows you the xp earned, any level ups gained, rare elements, outcome, and funding gained/provided by Cerberus. It's an interesting change. Oh, and loading screens are pretty awesomely done animated schematics so far.
Textures, lighting, everything graphics related is rather improved. I left the game in the middle of a conversation to help my wife, and she saw it and went "wow, that looks real", regarding shepard's face.