I prefer learning the kata as taught by the founder. There are several reasons I feel this way.
First, I assume that the founder (in my case, Soke Shimabuku Tatsuo) knew more about what he wanted the kata to be used for (bunkai) than is necessarily taught at my junior (brown belt) level. I don't presume that I know more than he did.
Second, I can change whatever I feel I must change to adapt to my own abilities and inabilities (based on things like weight, age, flexibility, size, etc) after I've learned to do it correctly in the first place. I feel it is difficult to learn the 'right' way as defined by the founder after having decided to do it one's own way.
Third, I have respect for tradition. If our tradition was to spit before stepping into the dojo, I'd spit. I really don't feel the need to be an individual when it comes to that. I see no harm in following tradition for the sake of tradition.
I understand that different people have different capabilities and limitations. However, I also feel that sometimes there are very valid reasons why doing something a way that might not be comfortable has value. For example, I am naturally splay-footed; always have been. I have difficulty with a good Seisan stance, and Naihanchi is a real challenge for me. However, I see the value of the toes-straight and toes-in stances and I have some limited understanding of their application. I will continue to do it 'the right way' and hope that I can eventually modify my abilities, rather than giving up and trying to fit the style to my capabilities.
I have seen with my own eyes what happens as kata is changed by instructors over the years. I know that Isshin-Ryu is quite splintered and there are significant differences in the way certain kata are done. I cannot say if this is good or bad; if it negatively affects the application of the techniques contained within the kata or not. But I know I can see the differences.
I am told there is a group of students who trained under a Sensei of great girth. They are now themselves instructors. There are hundreds of students scattered across the USA who do Isshin-Ryu kata with huge sweeping movements which were not in the original kata; they do this to clear their enormous bellies which they do not have; but their instructor's instructor did. Does it harm the application of the kata? I have no idea, but I can't guess it does it any good, either.
To give an analogy...
The Jewish Torah is written on a scroll, and it is copied laboriously by hand. It is over 2,000 years old. Recent copies have been compared to known examples of very early Torahs, and they are identical.
By contrast, the Old and New Testaments of the Bible have been translated into many languages, and translations have been made of those translations, and different translations have been made when one group disagreed with the translations made by other translations. Although all versions of the Bible say essentially the same thing, there are still significant differences in some areas; significant enough to cause great turmoil and anger among some groups. They're all, for lack of a better term, doing kata the way they feel like doing it. Is it still the 'Word of God'? They say so, but does that mean it is?