I do have a few suggestions on how these problems could have been addressed in this game.
1. Limit the number of players to 16 or less.
2. Ensure that a good number of players are active and competent enough for this game.
3. The dorm and the school should have been a single building or the connection between the two should have been a simple walkway instead of a train network.
4. A rule where no one is allowed to murder anyone for a certain number of days before the first murder and after each case. (2-3 days is recommended)
Keep in mind this is a common, simple forum game played for fun, with people here doing a bit more unique twists than is standard.
My thoughts:
The biggest factor in player limits is the work load for the host, or hosts (delegating tasks could allow for much larger player bases), and while it is harder to tell everyone apart when they pick game aliases (which is perhaps a bad idea), it doesn't really make the game harder to play.
This is a forum game and it should be expected that people will only make a few moves a day, or less. I'm not sure what you mean by competent, as it isn't like the base game does or should require any high-level thinking (as in the jab I made at your earlier post, if anyone caught it :P). These types of games should scale directly with the abilities of the players rather naturally.
Yes it seems generally agreed that the maps should be smaller. Having big maps seems fun, but it probably causes headaches for both the host and players.
It seems okay to limit some types of moves people can make, but killing is a pretty integral part of a mafia game. This would not only drag a game out for far, far longer than they do already (and more people would leave or lose interest) but would often be a very strange restriction when it came to plotting ( e.g. you have to plan your murder so that it can happen one phase from now, rather than now when you are behind your prey).
Also for activity, I believe a good deal of the people on this forum are college or high school students, and it /is/ kind of crunch time in lots of places now. When I start to feel like I have a lot of work to do, these types of things are the first I whittle out of my schedule to alleviate more time. I suppose I also don't feel much like there are many productive actions I can make at this point.