This isn't the place to discuss Mastercoin, but it may be worth pointing out an important difference here between Mastercoin's protocol and Counterparty's: every Mastercoin transaction has to have a small output to the Exodus Address (to which at least J.R. holds the private key). Counterparty has no such limitation.
EDIT: typo
Q1. I know you said this isn't the place to discuss MSC, but is the above true? Do you mean every future MSC transaction, (even once it's up & running) will have a small output to the Exodus address? That sucks.
Yes, it is true.
While we do appreciate donations, it may be worth pointing out that Bitcoin's development was not predicated on outside funding, and Counterparty is: 1) much simpler and smaller project than Bitcoin, and 2) relatively full-featured.
Most open-source projects are community-driven, with software developers contributing not primarily for the financial incentives, but because they really believe in the project they are developing (Gavin Andresen, for example, worked on Bitcoin a long time before being hired full-time). I will certainly be investing in Counterparty, but this is because I think it is a great project with lots of potential, not because there is a lot of money in alt-coins at the moment.