Hi there--
As an almost 30-year-old
Megan, I have a little experience with different pronunciations of it. Actually, I think that most of the time, the variety of pronunciations comes from where the person saying the name is from, not from the spelling. I mostly hear it pronounced somewhere between MEG-an and MAY-gan. Usually closer to the long A version (I live in a mid-atlantic state, so I don't know if that makes a difference). I've only been asked if it was MEE-gan by two people, one who knew someone who pronounced it that way (I don't know how it was spelled) and another who was from a foreign country and not a native English speaker.
Honestly, I'd go with
Megan just because it's the traditional (and simplest) spelling and it won't make much difference to most people on the pronunciation. I really don't think you'll have a problem with the MEE-gan thing. Chalk the other differences up to local accents. Not everyone says things exactly the same way, is it really that big a deal?.
Megan
--Side note: I'd heard that the actress who played
Anne of Green Gables in the movies,
Megan Follows, pronounced her name MEE-gan and was from Canada. That was the first time I'd heard of that. Maybe it's a Canadian thing?