Like your screenname, Kahless.

Many of these points have come up before. I've noticed several of them myself, during the game. However, I don't think Aeris was ever 'meant' to come back. That'd just cheapen her sacrifice, and the game's overall meaning, since many believe that Aeris' spirit was responsible for the Lifestream's assistance at the end.

I'll address several of the points in that article.

1) The presence of Aeris's ghost in her church is a very small plot point in
the game. In fact, it's barely discussed by any one in the game itself. Why
else would it be in the game. A nostalgic moment? Perhaps.
It's mentioned in the game that a person's spirit can often linger a while before returning to the Planet. Aeris' 'ghost' vanishes, or 'returns to the planet', as soon as you try to approach it.
2) Before the final battle there is an extra ledge that no one is standing on.
I saw that one. However, there are several smaller rocks too, which are also unoccupied. Why would there be an exact number of rocks available, anyway? It's not like the Planet had received a 'guest list' telling it how many people to expect...
3) For the battle against Bizarro-Sephiroth, if you are strong enough to form
three parties, then one party has only two characters. Each party should have
three members...
If you're strong enough to earn the 'three parties' option, then you're strong enough to fight with one under-manned team.
4) Throughout the game Cloud is in situations in which he must pick Aeris over
Tifa or show that he is an uncaring or a caring guy. However, after Aeris's
death, this entire point is dropped. Considering the number of decisions you
are forced to make (around twenty some) you would think it would have more
bearing than who you get to date...
Your choices do affect who you get to date at the Gold Saucer, whether its Aeris, Tifa, Yuffie or even Barret. They just decided to develop that 'love triangle' with Cloud, Aeris and Tifa in order to add more depth and emotion to the characters. If Aeris wasn't developed and involved as a character, her death would've meant a lot less.
5) In the Japanese version, why does Aeris speak at certain points after you
use the GameShark to get her back? Why does she only have it in certain spots?
The only one I've heard of is a single line uttered after the Icicle Inn snowboarding event. Apparently, they scripted these events - and the characters' responses - before they'd finalised exactly when the events would take place in the story.
7) Aeris's Umbrella has a higher Attack Power than her best weapon, the
Princess Guard, whereas everyone else's best weapon has a higher Attack Power
than all of their other weapons.
Cid's Flayer is stronger than the Venus Gospel, except it doesn't gain the same 'bonus' from Cid's MP. Aeris' ultimate weapon only really needs seven slots, since many players won't ave a huge number of strong Materia at that point. Still, I agree that it's odd that you get her best weapon so soon before her departure...
8) When you get Aeris's fourth limit break she has most likely already died.
If you actually do what you need to do to get it before she dies you waste vast
amounts of time (it took me three extra hours of getting her limit breaks up).
The point is that if you get it before she dies, it doesn't seem like you
should have it yet.
A conscientious player migth notice that many other characters can gain their level 4 limits in disc one, whereas she can't. Also, if they didn't give her one, then people would complain that this is inconsistent with the other characters, and that they wasted hours trying to find it...
9) Right before the pillar steps in the Forgotten City before Aeris dies there
is doorway in the background. If you look at the patterns on the pillar, the
doorway is somewhat similar but markedly different. Programmers usually don't
put extra stuff like that in a game; it's a waste of time and effort. There is
no way to reach the door.
There's also a cliff and a log tunnel just outside the Forgotten Capital that can't be reached. It's possible that they're part of an abandoned side-quest, or maybe they're just there to remind you that the world is even bigger than just what the characters can explore?
11) In the game manual there are FMV drawings of the characters. Every
character's drawing except Aeris (she is looking at the highwind you see it
where disc 1 is in) actually occurs in the game, or could realistically occur.
Aeris's cannot, as she wasn't with Cloud when he first saw the Highwind on the
first trip to Junon. She had already died when Barret and Tifa made their
escape on the Highwind later. In the picture she also dressed in white, and the
entire game she dressed in red...
She saw the Highwind, definitely. On board the Shinra cargo ship, she asks Cloud to take her on it someday. There's nothing 'impossible' about that picture... many of the character portraits aren' totally consistent with what's in the game. Barret and Marlene in Aeris' church, for instance, even though he never met her; Cid, sitting on the Tny Bronco in front of the rocket, apparently before the rocket's first failed launch attempt (notice how it's not leaning over in that picture?).
12) The strongest empirical evidence for this lies in a conversation Cloud has
with Tifa during on the bridge of the Highwind... Tifa:I wonder what Aeris
felt... when she was on that Altar... Cloud: I'm sure she wanted to give her
life for the planet... Tifa: Really? I wonder? I don't think that's it at all.
I think she didn't think she would die at all, but that she planned on coming
back all along. She always used to talk about the "Next Time". She talked about
the future more than any of us'. This is very, very suspect, as anyone can see.
Again, it heightens that tragedy - she had all those hopes and dreams extinguished. But then, her story didn't end with her death - her spirit 'came back' and helped to save the world in its time of greatest need.
The entire game is ruined, in my opinion, by the loss of Aeris, and the death
of hope and joy. Many argue her death insured the player's hatred of Sephiroth.
Even if she were to be theoretically resurrected, I would still hate Sephiroth.
In my opinion, Square should re-release the game with her resurrection, and a
better ending, one worthy of a Final Fantasy game. Would it make her death
meaningless? Yes, it would, her sacrifice would be null and void and hollow.
But her death makes the game meaningless... Judging by the number of people who
desperately want to resurrect her, I think Square would profit financially from
such a decision. A game, which was already great, could be made truly perfect.
But somehow, I don't think this will ever happen. - XxRTSmithxX.......(thx for
letting me share this falsehead)"
Sounds typical of a fan who can't get over the loss of a character. Re-writing the entire plot just to appease a few obsessives wouldn't be very useful, or good in my opinion. A "perfect" story where everyone lives happily ever after in peace and utter harmonious bliss is less meaningful than one coloured by genuine hardship and loss.