Both of them are great choices for long term investment, of course you cannot ignore Bitcoin. But for your question i will invest more in Ethereum, because of it's project. Almost all ICO are from ETH.
of course btc is so important at every other coin's value. but eth itself may manage to find a way to exclude itself from btc's price, mainly thx to erc20 token's icos. and nowadays vitalik says ethereum 2.0 is coming. let's keep watching them close.