Stuffing your altcoin's transaction data into the Bitcoin blockchain doesn't make it not-an-altcoin. The main sections are for the Bitcoin
currency and things that you can
directly do with bitcoins. If I can take my bitcoins, deposit them into your site, and then do something interesting without explicitly converting to a different currency, then your site can go in the main sections. For example, a casino could use a Counterparty currency as "chips", and this would be OK for the main sections as long as the casino could
automatically convert deposited BTC into these chips. Similarly, if someone was selling Overstock shares for BTC, then this trade would be OK for the main Marketplace regardless of the technology used to handle the Overstock shares. (But don't try any nonsense like saying that every unit of an altcoin is a share in a company...)
Noob question for sure.
If a coin or protocol isn't Bitcoin, then by definition isn't it an "Alternative Currency" ?
Is Mastercoin or Counter Party, Bitcoin?
Mastercoin is a normal scamcoin (more scammy than usual, in fact). Apparently it's common to transact in BTC using Counterparty, but Counterparty also has its own currency. I suspect that Counterparty has no really useful technology, but all I can find about their technology via Google is marketing fluff (bad sign), so I can't be sure. They both use the Bitcoin block chain for timestamping instead of doing their own mining. I think that this is often a good idea, but it doesn't mean that they're not altcoins (or that they're actually useful).
By the way, if you're already using the Bitcoin block chain, then why are you even creating a currency? Just use BTC. From what little I've read about Counterparty, it looks to me like their XCP was included just to enable pump-and-dump. (The BitDNS proposal that I co-authored in 2010 was probably the first to propose using the blockchain like this, but it just used BTC.)
Regardless of whether or not something is a scam, people building things on top of the blockchain is a reality. I can understand the 'don't bloat the blockchain' thinking, but by not engaging the bitcoin 2.0 crowd there are no productive discussions about how both can coexist- be it on the blockchain or on some sort of side chain, merge mining, etc, etc, etc.....