Hmmm. I don't see the problem in evaluating altcoins in btc. What you describe is a very short term mechanical raise or decrease of altcoins because of btc fluctuation. But in the medium/long term we can see altcoins have a real value on their own.

If you take ETH for example, last year in August 2016, it was worth 0.02 btc. Now it is 0.08 btc. So ETH was only multiplied by 4 ? Not at all! Because if you convert to USD : August 2016 ETH was worth $12. And now it is worth $250. Multiplied by x20.

This shows that ETH has "its own life" even if btc is used to value it.

The solution to not be "fooled" might be to evaluate altcoins in USD directly.

But this would be problematic for exchanges I guess, there must be a financial reason why they systematically use btc. And I am interesting in knowing those reason, if anyone knows.