1. It doesn't look like the prop ever stops; that wasn't fixed.
2. Nope, no ability to trim.
3. Yes, there is. Emergency blows are fun, if not practical, to perform. On the 688 (not sure about the others) there's the option to "Open" or "Close" the MBTs
4. Maybe in the LWAMI mod; unsure about stock.
5. Yes! You can put enemy platforms on the datalink with the antenna (receive with the floating wire), and let your friends handle some of the work. In fact, IIRC, some missions will have you finding and linking something so that the Ticos/Burkes can handle it.
6. Depending on the mod, sometimes.
7. No...no emergency flood. You can experiment with the MBT vent controls, but aside from that...
And as for the rest...that's Silent Hunter III/IV territory!

It's be amazing to have, but it'll be the devil to code.
Other advice: be sure that you patch to 1.04, then get the LWAMI modification, available at Mr. Bill Nichols' site
(www.subguru.com.) It fixes a number of problems and adds to the realism considerably. Beyond that, there's Alfa Tau and Reinforce Alert, both of which are currently the subject of intense discussion in the forum.
Oh, and before I forget: welcome aboard to DW, smack!