I filtered for about 15 years and thought it was great, then learned about ultralight backpacking; now I use tablets. (Chlorine ones have a lot less aftertaste than iodine.) No ill effects yet - knock on wood. I don't bother treating water that's going to get boiled for dinner. If the water seems too murky to drink before using tablets, it's not hard to use a bandana or something to filter it out first.

I do most of my backpacking in SE Alaska and around western Washington. Water has almost never been a problem to find, so I only carry 2 liters at a time. Don't know anything about desert climates. :\