When you are looking at buying a new flute, there are a couple of options that can help with the 3rd octave E.  The first is the split E mechanism.  The split E separates the action of the upper and lower G keys, allowing the lower G key to close when high E is played.  (Here is a link to a great illustration on Miyazawa’s website.)  This allows you to play the high E without worrying about intonation or cracking the note, especially when playing piano or softer.  It can also make it much easier to slur between high A and E.  The split E mechanism uses an extra rod, which can add a little bit of weight to the flute and it must be put on during the manufacturing of the instrument; it cannot be added later.  Some find that the extra weight is cumbersome and the extra rod that is required hits the right hand 1st finger.  Others notice that these issues go away after some time is taken to get used to the feel of it.  The split E is mostly available on offset G flutes, but you can get it on some inline flutes, however, some report that the mechanism causes binding on