To me the biggest difference is how bitcoins are created. It takes a great deal of investment in time, effort, money and energy just to mine and produce a single bitcoin.
I wouldn't even give too much credit to the mining of Bitcoin as a distinction between it and altcoin, who cares? Almost 20 million Bitcoins have already been mined, so the difficulty of mining doesn't affect anything related to its economics anymore unless we are only fooling ourselves.
However, Bitcoin and altcoins are not just mates, so don't let us compare much. Is it the pioneer title? Reliability? The true decentralization, unlike the rubbish we see these days? The preference of the big guys and institutional bodies? Name it. Bitcoin is just incomparable!