I just read a comment on amazon that said that the reason the er3 is so much cheaper than the er4 is that the er4 is manufactured and tested at Etymotic's facility, while the er3 are manufactured in china with the same material and drivers. So basically, they're made without the same strict quality control Etymotic normally employs. I wonder if that's true.
Etymotic is not going to let a product go out if it doesn't surpass their QC expectations. It's like getting a hand braided cable vs a factory braided cable. They are exactly the same, one just had a little bit more attention put into it. But if you put them side by side, you wouldn't notice a difference. China has come a long way from their cheap manufacturing methods.
The biggest difference between the two is the sound, cable, longevity, and accessories.
The ER4XR supposedly sound more balanced. I had the ER4XR, never heard the ER3XR. Meaning that it has the "boosted bass" (for what it's worth), but it still sounds coherent and doesn't seem out of place. The ER3XR, according to reviews, has it's bass boosted to where it's walking a tight rope between coherency and sound off. So this will depend on you. I would've liked more bass from the ER4XR, but what that meant for me was leaving Etymotic alone altogether.
The cable on the ER4 is braided, the ER3 is not, but both are solid, and the ER3XR cable should cause less noise when it comes to rubbing on course surfaces like a jacket zipper.
Longevity just means that I expect Etymotic will put precedence on their flagship more-so than their next in line. Meaning that over time, you'll probably be able to get filters and repairs for the ER4XR, where the ER3XR might not in favor of it's newer variants down the line (most likely a non-issue).
Lastly, the ER4XR I think brings more accessories. But for the price difference, you could probably just buy them separately if you really need them.
Hope this helps. I did a lot of research before deciding to go with the ER4XR and not the ER3XR and in the end I was still unhappy with them (Not Etymotic's fault. Just not my type of sound signature).