For one, there's absolutely no proof those letters are real. It's outdated speculation that sounds just like what that one guy said, in regards to Aerith being able to be resurrected in the original version of the game's design, but then was taken out when released. That turned out to be a hoax and was also supposedly from some unnamed employee of Square.
Furthermore, that directly contradicts their original idea of who Aerith's love interest was. According to the creators, it was Sephiroth. Then they decided to make it Zack. There has been no commentary at all that states Cloud and Aerith were to fall in love. The creator's have spoken quite extensively of what Aerith's role in the designing days of FFVII were, and that was never mentioned at all.
I don't think I really have to go into how Aerith living or coming back in the end would severely cheapen the impact of her death and the entire point her death was included in FFVII in the first place. It not only served in making the storyline memorable and emotional, but also stood as a statement regarding the death of characters in RPGs, specifically in FF. Its theme was life and how death could come in an instant and without warning. Not only that, but that it was permanent. They'd be going against their own theme if they revived her.
If you want to read some facts regarding the development of FFVII and its characters, check out our site's Ultimania Omega translations of the "Early Material Files" which look at the designing of FFVII. It's here.
http://thelifestream.net/tag/final-fantasy-vii-ultimania-omega-translations/
And if you want more insight into all of that and how Sephiroth became unhinged, that's what Crisis Core is for
Also, there really aren't that many plot holes or unresolved questions regarding FFVII's ending. You can attribute that to either misunderstanding of the storyline or just a bad localization. It's not really that mysterious at all.