From my experience, I'm not liking the implementation at all currently. I've embarked seven times. All seven times, I've had 1-4 of my 7 starters with some kind of disorder/disease instantly. I got a skitzo in my current one, along with a disease (seems to be flu like from the description).
The main issue I have at current isn't the diseases per say, but the ability for them to spawn on your starter 7, and first two migrant waves - it forces you to shift focus from building and survival, to rushing for a hospital to try and stop that skitzo from causing a rampage, or that disease causing deaths in the first year that causes unhappiness, and inevitably, a disaster that's out of control. For a more mature fort (1 year or more) - it SEEMS to fit well, but I need to play test a bit.
My skitzo just went nuts and tried to club a drake to death, who promptly murdered him and causing a massive negative mood... not even summer year 1, I'm down a dwarf and in a sharp negative happiness spiral due to the skitzo...
Positive note wise:
~ I do like the genetic 'differences', midgets, giants, blind dwarves, and similar - but at 0.1% that's too rare imo. should be more along 0.8-1% (1-2 of these possible in a 200 man fortress on average).
~ I do like the addition of having a hospital and its purpose.
~ I do like the added challenge/risk of migrants, traders, and similar.
~ I especially like rabies. If it works as I read it, I intend to infect a dozen+ dogs or similar, stick them in a cage, load said cage into a catapult, and fling it over my walls onto siegers to spring a swarm of rabid, crazy berserk dogs on them partially to kill a few, other partially, to watch as rabies spreads to them, and they tear themselves apart inside out
Sorry, but picture a cage with 30 mastiffs inside frothing at the mouth, flying out of the sky over a wall at you...
~ further the concept of biological warfare on enemies, if some were deadlier/faster acting (need to test if some are), is quite exciting. Can't break that siege of orcs? Throw a smallpox infected victim outside!
At the worst, it weakens them for your defenses. At best, it kills enough they run away.
Negative Notes:
~ I don't feel medicine specifically for 'cancer' is needed, when it's a single 'issue'. Seems redundant unless you plan to expand that, and I'd argue the list is already a bit large. More wouldn't do any good.
~ Early diseases/issues in starting dwarves, and first 2 migrant waves makes the game (for me) shift from growth and building, to rushing to get a hospital up to try and control the damage of diseases and lunatics are causing.
~ The act of creating a 'migrant fort' then a 'main fort' AND possibly a 'nutcase fort' just to try and stop the insane damage of the possible diseases leads to a lot of micromanaging, which I feel is not a good thing. Though, I do understand the intent. I actually find it in a sense, amusing to setup a 'ward' for the nutcases and watching the drama of it play out... I'll reflect properly on this after a good 10 years of playing.
Suggestions:~ Shift some of the diseases over to events, like when harvesting plants, killing specific enemies, hell, even weather, clouds, contaminated water, various things naturally dwarves do/interact with, that a have a small chance to start diseases and problems. This keeps the 'threat' of diseases constant but marginal, as once migrants are done arriving, and you contain it all, the threat basically vanishes beyond traders (or siegers, but cant' say how common sick siegers/traders are). I would argue the 'subtle' diseases would be far rarer to avoid annoying constant infections, but still, keep that threat around. You can argue traders/siegers can't be avoided - but Siegers can be dealt with in a multitude of ways avoiding contact, same with traders with a very simple airlock design I've utilized for a vampire fort - takes maybe 50 blocks, 2 mechanisms, and a door.
Possible Bugs:~ Insomnia seems to be incredibly common. of my 7 embarks, I've had 6 dwarves with it now. That's a small scale to come off of due to rng, but that's WELL over the % it should be.
I'll update this as I get experience with it properly.
P.S.
~ I like the concepts for rabies/diseases from wild animals/bites (if rare), vermin bites having a chance to cause a disease, and most of your suggested changes.
~ I don't agree on a 'ward' that cures everything, as it's simply too overpowered unless it has some serious draw back or limitation. i.E. it lives for 1 season, it causes dwarves to be dizzy for a year, or something sharp as a trade off for 'all around' immunity/cure. I feel this way about armok's ward - it's like 27 points at embark, and totally nullifies any form of 'secret fun' with no effort/cost.
Edit:
Yeah... this is really buggy... I unpaused the screen, and this happened before I could even see wtf was going on. Just embarked.
http://i.imgur.com/6cHcHZq.pngAlso my entire starter team is now infected with a disease... and unhappy due their buddy being torn limb from limb.
Edit 2:
And I see this in combat log... don't think this is right...
http://i.imgur.com/m7u4af3.pngI don't think he's supposed to go unconcious almost 1000x, or similar matters.
The spam from diseases and such is driving me crazy too, as I can't tell when a legit threat is appearing (watching the icon on the top left) as this spams it non-stop by combat log.