Pulling a lever breaks sneak and always has. Yeah it's kind of dumb but if this wasn't the case, absolutely nothing would prevent even average stealth users from completing quests with zero effort. If it didn't break stealth then nothing except required kills and spiders would prevent me from just waltzing to the final boss.
Mobs do drop aggro, you just need to use invisibility or you need to leave the general area the mob is in.
Movement penalties have, again, always existed and I agree it wouldn't be a bad idea to remove them (with enhancements).
Auto aggro after Assassinate existed before u17, and u14. After Assassinating without drawing aggro was removed (which was u19 I think), the ability to shed aggro by, you know, running away, made it better than it was before. This is something I would consider unbalancing if it were the case, being able to Assassinate whole dungeons with out anything attacking you. A compromise would be to give bonuses to Spot to mobs in the vicinity of an assassinated ally (woah hey Bob dropped dead there's something fishy going on) but not have them instantly aggro, or have a "critical Assassinate" not draw aggro. And double-assassinating is still possible, you just need to Bluff the second target.
Unless something has changed in the last few months (I've been doing nothing but eTRing for awhile), I just don't believe the stealth system needs any major changes. I can do some tests later to confirm what I'm saying (or just find that I'm wrong, which I doubt I am).
This video from u22 shows a couple things I'm talking about (shedding aggro mostly).