These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
They Changed It, Now It Sucks: There is some trepidition because the editors in the letters' pages have implied that they will continue writing Mainstream-Ultimate crossovers. One of the reasons why the Ultimate universe is popular, and one of its distinct qualities, is that it is untouched by outside universes, giving it a lot more freedom in development. Opening the floodgates of crossover-dom may turn it into just another alternate universe, is one opinion.
A lot of fans also dislike that it's the post-One More Day Peter that crosses over with Miles, rather than the more accomplished, Happily Married version, who would have been a better role model and inspiration to the new Spidey.