As a fellow "simulationist"...
1) Is there a way to remain bad at a skill with advancing levels? I know that all skills (and ability bonuses, etc.) advance automatically at 1/2 point per level, so on the surface of it, I would have to assume that the answer is negative, but perhaps there is a flaw system, or some other system to enable characters to remain bad at given skill(s).
The DCs scale with level also. Some tasks will be easier -- ones that were hard at level 1 will be easy at level 20. However, tasks that were designed to be moderately difficult at level 20 will be moderately difficult, so the +5 trained and +3 skill focus will make a huge difference even at higher levels. This is the same way skill vs skill works - because both sides get the same level modifier, you'll basically be the exact same level of "badness" against equal level foes. Yes, your level 20 guy will have a better chance of spotting the kobold than your level 1 guy would, but his chance of spotting a level 20 stealthy guy will still be poor without training and a good wisdom (or skill focus).
2) Is it true that most of the problematic but interesting spells and effects are gone (a select few being converted to rituals) or modified beyond recognition as seemed to be the case from the previews? (e.g. Baleful Polymorph)
Yes and no. The really powerful ones are - like polymorph. However, there are plenty of powers that can still be used in interesting ways. The fact that wizards get infinite access to things like prestidigitation (which has been greatly expanded in scope) and mage hand will allow for some good creativity. You'll be less likely to see game breaking high power flexibility. As a simulationist though, this is great for me - because it fixes issues I had with 3.5. It's only bad if you're also a power gamer.
3) Are the per-encounter powers explicit per-encounter powers, or implicit per-encounter powers?
They are explicity per encounter (I'm not sure how you could have an implicit rule that states "Once per encounter you may...").
I can rationalize the martial stuff by thinking of it as "it's basically impossible to pull this off twice against the same crowd in a short period of time," however, this does not apply to all powers nor to spell casters (for me). If you were okay with 3.x wizards simulating "reality" though, this shouldn't be a problem. I've hated D&D spell casting for a loooong time, and always used my own custom system since 2e. However, 4e doesn't seem as hard to "fix" so I actually just plan on allowing wizards to treat their encounters, dailies, and utilities as spell slots (kind of like the 3.x sorcerer). Dailies can be traded down for encounters, and encounters for utilities. It's how much magic a mage can control without getting worn out. He recovers encounter slots after 5 minute rests -- those are easy to recover from -- daily slots take so much out of the character that they require a good day's rest to get them back. I don't think it should be game breaking as in theory dailies are supposed to be equal in power. Yes, it'll make casters more flexible, but I'm okay with that.
4) Since hit points are now even more abstract than before, is there a system for more persistent injuries (that only heal slowly or with the aid of magic)?
Just like 3.x, there's no rule for this. I implemented custom rules for 3.x for my games, though I find the rules for 4.0 MUCH easier to work with in this regard. I'm simply going to say that once you hit 0, you are
wounded: you are -2 to all actions and can only spend one healing surge per day (and must make a death save for it to work). You are no longer wounded once you reach max HP. I may make it -5 to actions until you reach bloodied, then -2 until you're at max. I haven't needed to do that yet. I find this much cleaner than what I had to do under 3.x, especially since 4e damage is much more controlled.
5) Have most of the non-combat abilities of monsters, creatures and NPCs really been removed as previews seemed to indicate they would be?
There weren't any to remove, as far as I'm concerned. They are description-lite in many cases, but I never really needed or used rules for habitat, feeding, and other non-sense that was tossed into some of the 3.x books. I knew how they interacted in my world. Personally, I like 4e monsters because it's easy for me to find the stats without digging through tons of garbage I didn't want and then wrap them in my own design - which is what I did in 3.x. In reality, I didn't use many 3.x monsters because they were such a pain to tweak to work the way I needed. I did what 4e does: I create a creature with the abilities that I want. This is the first edition in a while that will actually allow me to use the monster writeups in the MM for something other than just ideas.
To be blunt, your questions strike me more as someone that doesn't like change, not so much someone that likes simulation. I also think you are wearing rosy glasses if you think 3.x had most of the stuff you imply that 4e should have. No version of D&D was built for my simulationist leanings, so it's always been a question of how much do I have to do on my own and how hard is it to do it. As a general rule, 4e is FAR easier for me to make simulationist than previous versions of D&D. There is one exception to this though... powers.
If you want to find something to grouse about, it's powers you're looking for. They are THE most irrational thing in the game. Not the per day, per encounter issue - that's very easy to address. For me, the problem is things like a rogue shooting up to 9 targets in one standard action with a crossbow or... 9 daggers. That just makes no sense. It also doesn't make sense that it blinds every target. I mean, okay, even if he somehow managed to hit all 9... he hit them ALL right above the eyes so that they end up blinded by the blood? It's THAT type of thing I'm going to have the most issue addressing. Most likely, I'll just eliminate access to certain powers just like I had to do with most 3.x spells. I'll probably create a couple to take their place. Most powers are FAR more reasonable, but this, imo, is the biggest problem with 4e from a simulationist stand point. Yeah, square fireballs are goofy, but that's so easy to address there's not really any point to even talking about it.