It may become a matter of semantics, but updates are necessary and I don't have a problem with simple revisions that may be similar to things done in Ultimate or other recent storylines.
In the case of the FF, the origin obviously needs to be updated, but I would keep it as close in spirit to the original as possible. But the nature of the characters shouldn't be changed. Ben and Reed met in college and it makes just as much sense to have a football player and a brilliant science student meet in college in 2013 as it did in the 1960s
Doom should still be Doom and Galactus should still be Galactus. Again, some updating is fine, but don't completely change the nature of the characters.
I wouldn't consider some reasonable updates bad - whether they look similar to Ultimate or not - but I wouldn't consider that 'basing' the film on Ultimate FF.
The film should be based on the most enduring elements of the characters. Influences from Kirby, Byrne, Millar etc. are fine, but it certainly shouldn't be based on a series that is completely out of step with 50 years of history.
This bold statement is the core of updating, imho. It is a true statement, but audiences today honestly buy in less to such contrivances as a nerd and a jock meeting off screen and becoming besties. So what worked in the 1960s doesn't actually work today, even though it's just as plausible as it was back then, the level of plausibility is raised - as far as human interactions. Let's not have the fallacy of 'they accept aliens, so they'll accept people who have no reason to be friends being friends.'
And while you may not consider things being 'based' in the Ultimate universe, the fact is that it inspires costumes and story most strongly. It keeps the spirit of the original completely intact, but it changes a lot of the details. Instead of keeping all the enduring elements, it keeps the spirit that made those elements enduring and sometimes applies those to new elements.
Galactus being some bugs doesn't change the spirit of the character at all. Even Doom's goat legs don't change the character as much as he having powers does (a change I dislike strongly). There's little point in holding onto enduring elements that can be off putting on some level when you can have the spirit that made those elements enduring and apply it to things that are more modern, even if they haven't been in 50 years of comics.
FOX is probably still attempting to work out a budget, and the rumored script problems are a reflection of this. Big screen superhero spectacles are pricey - TA, TDKR, ASM, IM3, MOS, DOFP, GOTG, B&S and A:AOU all either had or will have budgets greater than $200 million. Unless Trank (with just one film under his belt) has filmmaking knowledge that somehow has eluded Whedon, Nolan, Webb, Black, Snyder, Singer and Gunn, a proper portrayal of the FF is going to cost beaucoup bucks. With the prior two FF films performing modestly at the box office, and the last two FOX X-Men films underperforming, FOX is either going to have to cut corners and hope for the best or (please oh please oh please) relinquish the rights.
Superheroes, have different abilities. Just because Magneto, and Namor and Colossus and Beast and Iceman are powerful mutants doesn't mean they can read minds. A mutant, even one with limited experience, like M, is a better choice to read minds, because they've shown that that's what they do. Now, it's true, many of those most powerful characters could read minds if they really wanted to, but they don't have any motivation or need to do so, and thus even less experience than M reading minds, even though they're much more accomplished mutants. M does, so bringing her in to read minds is not hoping for the best or cutting corners, it's getting the best person for the particular job. The more specific the job, ie making a great big SFX movie on a limited budget, the more specific experience is valuable rather than general experience of being a mutant/making movies/whatever. Now, you could bring in Beast to read minds, because he's got so much experience as a mutant, and he might be able to invent something that could read minds, but that would be a crapshoot, that would be hoping for the best. Now, some people in the comics universe feel like all mutants have the same powers, basically, so one mutant is just as good as another, and the make no distinctions between them. This is just not true, and generally we accept that those characters just don't understand what it is that mutants do.
And remember, the article you showed me that explained in detail why a high budget would be bad for Fantastic Four?
Imagine if FF was never in danger of being skewered over the summer? The concerns you brought up earlier, nearby releases, may never be a problem for this franchise. That's a good thing, and bodes well for it's success. There's no script problems or budget meetings, it's just Fox getting someone who made a great movie with lots of FX and scale and most importantly heart without spending a lot of money to do it again. It's just that simple.