Would it be better if it didn't flash? Yes. But, as other have said, you get used to it. I still notice it, but don't really think about it.
The next reader technology will solve the problem, and more screen choices are in the near future. The choice now between eInk and LCD is really one of personal preference. Both have advantages and disadvantages. You just go with the one that is the "lesser of evils" for you.
I am really pretty neutral. I seldom read in direct sunlight (it amazes me that is so important to most people) as here in Texas the last place I want to read is in the sun. A shade tree is a must have. On the other hand I do read at least 25% of the time is less than perfect lighting conditions. So the back light of a LCD is great. But, I like to read more than a few hours sometimes, so the LCD battery life is a killer (I have my doubts the iPad actually gets 10 hours in real life, we shall see). I like the clarity and over look of eInk, and my eyes seem to read longer without tiredness.
Bottom line is you just have to work at it, and find the option that is best for you.