Well, I am not a landlord, but expecting tennants to leave the apt in the exact way is was 2 years ago isn't really possible, is it?
Carpet stains unfortunetely do happen over a time period, and carpet does wear after a few years so then the next tennnants that move in, when they move out, the carpet would be even worse. It would actually be better to have wood floors, then as the tennants move out you can just re-sand and varnish them and they are as good as new. Don't you think living with someones elses carpet is a little disgusting anyway?? Apartments ALWAYS need to be painted before new tennants move in, that shouldnt be the tennants responsibility. Who ever heard of a tennant painting an apartment, then moving?? Regular holes for pictures, curtain rods, shades and blinds, obviously are to be expected, a little dab of plaster should do the trick, plus the new tennants will probaby make the same holes.
Obviously is the apartment has huge holes and major destruction has happend, then security is held, but regular wear and tear that is easily repaired shouldnt be a big deal.

The key phrase is Reasonable Wear & Tear. Damages are a different story.

I've kept security deposits, and taken tenants to court for stain and burn damage to carpets and flooring when the damage was excessive.

Security deposits don't even come remotely close to covering damages caused by irresponsible tenants.

Here is a link that might be useful: Wear & Tear Vs. Damages

Where I live it is not allowed to charge tenants for carpet cleaning or painting. It is illegal. It is considered 'normal wear and tear' that a landlord must absorb. The carpet is going to get dirty and the walls are going to get dingy no matter what, so a landlord should factor in these costs as part of property maintenance.

If the place is so damaged that a major overhaul is necessary - huge holes in walls, carpet stains that won't come out from a cleaning, broken windows, appliances that were not cleaned at all, ect. then you can deduct from the deposit.

I don't see the problem with nail holes as they can be touched up easily and painted over. IF you had it in your lease that there were to be no nail holes whatsoever, and many leases do stipulate this, you may have a good case to fight.

Like so many questions posted here, you must really go to your local sources for info as laws vary from state to state, and city to city.

I don't know which of your damages count as wear and tear, but I will say these things:

a landlord should provide window coverings; if they do, then clearly any EXTRA holes in the woodwork is damage

Painting the apartment so it's fresh, and I think even cleaning the carpet, is just something that landlords do as part of the work involved in this form of business or income (even if it's not actual profit, it's still income).

(Painting the apartment to cover the patching of excessive holes in the walls, I would want to be reimbursed for)

I would expect to have to do a basic cleaning, even if the tenant left it broom clean. I'd only be looking for money back if they left it really grungy.

Personally, a picture hole or two would be somethign I'd roll with.

It would actually be better to have wood floors, then as the tennants move out you can just re-sand and varnish them and they are as good as new.
Isn't that a lot more money, and work, than carpet? Also, you can only refinish floors so often, or you start to wear away too much! There are some commercial finished (Bona Kemi's Traffic) that are tough AND are repairable, so you don't have to redo the whole floor. As a renter, I would not expect to have brand-new carpet.

Did you document the things that were messed up? Here's where a video camera would be really handy!

You need to check your state's law's, as mentioned, to see what is expected of you. Learn them well ;) My state recently changed it's laws and now repainting and carpet cleaning are the landlord's expense to bear. I have no problem bearing the repainting, never did. The carpet cleaning bugs me. I don't like cleaning up other people's dirt, and to me cleaning a carpet is just that. But it's the law, so be it. (As a homeowner, before we got hardwood I cleaned our carpet every 6 months. Boggles my mind the filthy water I've seen come out of rental carpets, and how some tenants will tromp all over the carpet with shoes on, let their kids crawl on that tracked in crud, and not clean it for their own comfort while living there. Gross, imho.) Anyway, do check your state laws on that one.

243 holes is excessive, no matter how you look at it. In a 2 br with l.r., kitchen and bath, that's almost 50 holes per room. Who does that?? Were it me, I'd charge for the labor for all those. What are "unidentified" holes? Larger ones? Drywall damage? You can charge for those. $10/hr is on the low end. If the carpet were only two years old, and it was excellent when they moved in, and now 3 stains won't come out and it's ruined, yeah, I'd charge for that. Because they took it over at the infancy stages of it's life span, not the end of it. Carpeting has gotten quite expensive, and average life span is 7-10 yrs. Could be less in a rental unit, I suppose, but you should get much more more than 2 years out of it.

It would actually be better to have wood floors, then as the tennants move out you can just re-sand and varnish them and they are as good as new.. Two of our rentals have original oak hardwood (nearly 80 yrs old) the other is carpeted. I'll take the hardwood any day for between tenant cleaning. However refinishing a hardwood floor is not a job meant to be done regularly to maintain it, while shampooing a carpet regularly extends the lifespan. Refinishing is costly, messy, and not feasible if it's not solid hardwood either. (Engineered hardwood allows for 2 refinishes in its lifespan.) Doesn't stop the damage, either. It got so bad with tenants drilling holes through the flooring to the basement to run cable wire because they didn't like the location prior tenants used, I had to put a clause in the lease that there would be no hole drilling in floors. In one house there are at least 11 holes drilled between l.r. and bedrooms (7 in the living room). One guy apparently used a mini auger to drill a 2" diameter hole to run a stupid cable wire. It's also expensive to refinish. I was quoted $2k to strip and refinish two bedrooms, living room and hallway. I wanted to do it because a tenant had a cat there (against permission) and it urinated on the floor and as a result left 'scorched' or blackened spots. I managed to get out 70% of those marks with a product from HD, but flooring guy urged us to wait till it was no longer a rental to refinish.

Do you have photos/video of before and after?

If you're being sued, you'd better take pictures and get receipts for everything you spend. Having had a rental property once (and ONLY once), I feel your pain. No reason ever for that many nail holes. If you don't have proof, you may end up having to give the deposit back.

I'm in Florida and at least where we are living, when we move we're required to hire a professional steam cleaner for the carpet (and provide a receipt) plus we have a whole legal size sheet of paper listing what's to be cleaned (with places you can check them off as you finish them). I'm thinking Wisconsin sounds pretty good right now--haha, bud! We're moving in a little over a month, and I'm hiring Merry Maids. Bless them.