Personally, I believe that I do not like web applications that are (usually) disguised as iOS apps. I tend to notice a lot of discrepancies between the web application user interface and the native application, and most of the time it bothers me (my biggest pet button pressed a button and saw that it stands out with a small translucent black box around it, like a link ) Now I canβt imagine the main demographic user, who probably doesnβt care, but this is my personal opinion.
From a programming point of view, I have never written a web application before, but I assume that it will be slightly less structured than the native application, just because writing HTML, Javascript and CSS does not make you assume a specific project structure, unlike applications iPhone, which have various types, controllers, etc. Depending on what you want to write, it may be liberation, but it can also get confused very quickly.
As the middapark said, you can also use a mixture of the two systems if you want. I mean, I assume that you are as good a web developer as an iOS developer. If you are stronger in one suit than in another, then I say that you should lean toward a direction in that direction. I'd rather see a superbly written web application than a poorly written native application, and vice versa.
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