First lets look at a couple things that Fox and Trank set out to do with their Fantastic Four:
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Create a more grounded, sci-fi heavy world
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A focus on characters and family
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Potential for sequels and crossovers
Given this I have taken some elements of the movie, its general ideas, story beats, and tone and crafted my own take in bullet form/summary:
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Most of the first act of the movie occurs as it does in the film with two major changes: Doom does not return to the Baxter Foundation (in this version we start at Central City Foundation, also in NYC) but rather, after experimenting with the original Quantum Gate was horribly scarred and fled to his home country of Latveria (which, through exposition, is said to be on the verge of civil war); Victor has not been seen since
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Sue travels with Ben, Reed, and Johnny to Earth Zero where all four get their powers
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The four (barely) make it back to Earth and the power-discovery/body-horror scenes remain and are expanded
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Reed does not flee
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The 1 year time jump remains and the team have begun to manage their abilities while remaining in government isolation
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Greater emphasis is put on the team bonding, Reed and Sue becoming closer, and Reed searching for some sort of cure, etc...; Their isolation forces these characters to bond
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Meanwhile in Latveria a civil war has occurred and the new and mysterious leadership presents a major threat to the surrounding regions as there has seemingly been a massive increase in weapon development of an unknown variety; the US government sends in a military team to take out the leader of the group, a man called “The Sorcerer” by the locals; the military unit finds "The Sorcerer" - revealed to be Dr. Doom (who gained powers from his experiments with the Quantum Gate, and is now clad in armor); Doom kills the military unit
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Learning what has become of Victor and his new found abilities, Harvey Allen convinces the US government to send the Fantastic Four to retrieve Victor; at first hesitant, it is actually Franklin Storm who convinces the team to retrieve Victor (feeling guilty for what happened to his former protegee)
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The four travel to Latveria, defeat some of Doom’s henchmen, confront Doom and fight; the four are defeated and retreat back to Central City
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While reeling from their loss, Doom attacks Central City and initiates the Quantum Gate in order to destroy NYC (angry that the military and the FF dared to try and stop him in Latveria, personal issues with Reed and Franklin, etc...); Franklin is killed
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The four and Doom are sucked into the Quantum Gate and end up on Earth Zero
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The final battle occurs largely as it does in the movie with the four defeating Doom as a team; Doom is seemingly destroyed and the gate closes as the four escape
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The FF return to NYC and are greeted as heroes by the public
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The ending occurs as it does in the movie with the FF separating from the US government and this time are given full control of NYC’s “site B” known as the Baxter Building; they officially dub themselves the Fantastic Four
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Meanwhile back in an underground bunker in Latveria, Doom is revealed to be alive and well and the “Doom” that the FF fought was actually a Doom-Bot; it is further revealed that Doom has been manufacturing an army of Doom-Bots (i.e. the unknown weapons that were being developed)
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In a post credits scene, Reed develops a second gateway - one that would allow them to view and possibly interact with alternate realities; possibly setting up an encounter with a particular reality that had a few well known mutants *wink* *wink*
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The costumes again would be somewhat more realistic (I liked the idea of the containment suits but they could have been a tad more comicbook-ish):
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While I actually liked Doom's unique design in the context of the movie, again something more comicbook-ish yet modern would be nice:
Ultimately I feel these story and design changes would meet Fox and Trank's desires to make a Fantastic Four movie different from other live action versions but also would make comic fans happier and be a better structured movie overall.
Overall I felt the actual movie was ok (very average, run of the mill stuff) but could have been much better.