What's the best Cryptocurrency to invest in long term? Why?

Ethereum has the best long-term potential of any cryptocurrency. Right now Bitcoin is still king, but I think Ethereum will become #1 in short order.
There were 162k transactions on the Ethereum blockchain on 5/19/2017.
Confirmed Transactions Per Day
There are already almost half as many transactions on the Ethereum blockchain as the Bitcoin blockchain, and Ethereum is growing exponentially, while Bitcoin has reached its maximum capacity for now. Cryptocurrencies, like social networks, have extremely strong network effects. As the adoption of Ethereum continues to grow, its utility and value will grow exponentially..
Extremely bullish? Well in this case higher is not better. The mempool consists of all the data from Bitcoin transactions waiting to be confirmed. There is currently a backlog of almost 3,000,000 transactions! Bitcoin can only process a maximum of 7 transactions per second so it would take approximately 5 days to clear the backlog if no new transactions are made. Even though more and more people are introduced to Bitcoin every day, the network can’t handle any more transactions. Because of this, many developers have chosen to develop their apps on the Ethereum blockchain instead. In the case of Storj, they actually moved from the Bitcoin blockchain to the Ethereum blockchain because of the network congestion and high fees.

Even though the price of Ethereum has already appreciated significantly in 2017, there is still 10x, maybe even 100x long-term upside from current levels. Ethereum hasn’t come close to mainstream adoption yet, but there are hundreds, possibly thousands of applications in development. Many of these applications are focused on making Ethereum more accessible and user friendly. The world wide web was extremely inaccessible in the early days until Netscape came along and made it much easier for the general public to browse the internet. As the experience of browsing the web became much more accessible, usage exploded. Ethereum hasn’t had its “Netscape” yet, but it is in development. As these projects come online over the next few years, millions of people will be introduced to Ethereum, and the its value will skyrocket.

While the general public is just becoming aware of Ethereum, it already also has the backing of major global corporations. The recently formed Enterprise Ethereum Alliance consists of giants such as Intel, J.P. Morgan, and Microsoft. Since the EEA launched on Feb 28, 2017 they have received hundreds of new applications for membership. They are expected to announce the new members in the near future.

There will likely be some growing pains along the way, but Ethereum has a great development team. Ethereum’s founder, Vitalik Buterin is very well-respected and most people in the Ethereum community believe in his vision. Having a strong leader at this stage in development is extremely important because protocol upgrades can be much more easily implemented. Since Ethereum is a relatively new cryptocurrency, its developers have had the opportunity to learn from mistakes that Bitcoin and other earlier cryptocurrencies have made and have plans to preemptively solve them.

Here are some of the upgrades that are currently in development:

Scalability improvements - Raiden Network makes 1,000,000+ transfers per second possible. Ethereum can currently handle about 15 transactions per second, while Bitcoin is limited to around 7.
Anonymous transactions - Zk-SNARKs will dramatically improve privacy by enabling completely anonymous transactions.
Transition from proof-of-work to proof-of-stake - This will prevent miner centralization, protect against 51% attacks, and decrease the inflation rate.
The Ethereum protocol is continuously evolving, there are myriad applications in development, and the user base is exploding. I don’t expect there to be only one “winner”, but if I had to bet on one horse it would definitely be Ethereum.