After countless attempts, Godzilla finally ended up in the hands of an American film company in 1998. With the blessing from Toho, Roland Emmerich and Dean Devlin set out to make the their own version of the movie Jan De Bont failed to make a few years prior because of budget concerns. As such, the two makers of Independence Day destroyed any attempt at creating a franchise and all hope of Godzilla fans finally seeing their favorite monster in an epic, big budget classic.
The problems, for the most part, all stem from this bastardized version of "Godzilla" itself. The thought of a giant monster rampaging through a heavily populated city should be terrifying. With a stack of goofy characters from the human perspective, Godzilla walks along city streets without so much as knocking over a telephone pole. Damage is pushed into the hands of the incompetent military who, after easily missing countless opportunities to kill the creature, somehow get it right in the end.
That's the other major problem (aside from the ridiculous and unnecessary design of Godzilla) that completely changes the purpose and point of the Godzilla series. He can't be killed since, when he is, it defeats the whole point of its existence. Yes, this "update" is created by a nuclear test, but that's the last of it. There's not another line in the movie that brings this up.
The plot holes and logic gaps are numerous enough to cause an aneurysm. It's understandable that when you have a giant iguana casually strolling through New York, you don't need much in the way of intelligence. However, a lot of the action revolves around flat out stupid logic, such as Godzilla's ability to snap a helicopter in two but not a cab containing the lead actors. It destroys what little excitement the movie had going for it. The same goes for the extended sequence in Madison Square Garden that shamelessly steals from Jurassic Park, killing the sense of scale which is about the only positive thing to come from this.